From 8d173567a5298982a211b30a713061c0d676c93a Mon Sep 17 00:00:00 2001
From: Eric Marcon <eric.marcon@ecofog.gf>
Date: Fri, 9 Feb 2018 15:39:08 -0300
Subject: [PATCH] Delete library.bib

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-Automatically generated by Mendeley Desktop 1.17.13
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-
-@article{Brunet1997,
-abstract = {Une premi{\`{e}}re approche syst{\'{e}}matique des discontinuit{\'{e}}s a plus de trente ans. Elle s'attachait surtout aux discontinuit{\'{e}}s dans les dynamiques, aux dialectiques quantit{\'{e}}-qualit{\'{e}} et aux limites de syst{\`{e}}mes. Les rapports avec les discontinuit{\'{e}}s observables dans l'espace g{\'{e}}ographique, et les sauts marqu{\'{e}}s par les statistiques spatiales sont pr{\'{e}}cis{\'{e}}s par la discussion.},
-author = {Brunet, Roger},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brunet - 1997 - La discontinuit{\'{e}} en g{\'{e}}ographie origines et probl{\`{e}}mes de recherche.pdf:pdf},
-journal = {L'Espace g{\'{e}}ographique},
-number = {4},
-pages = {297--308},
-title = {{La discontinuit{\'{e}} en g{\'{e}}ographie: origines et probl{\`{e}}mes de recherche}},
-url = {http://www.persee.fr/doc/spgeo{\_}0046-2497{\_}1997{\_}num{\_}26{\_}4{\_}1096},
-volume = {26},
-year = {1997}
-}
-@article{Lavorel1997,
-abstract = {Predicting the effects of anthropogenic changes in climate, atmospheric composition and land use on vegetation patterns has been a central concern of recent ecological research. This aim has revived the search for classification schemes that can be to group plant species according to their response to specified environmental factors. One way forward is to adopt a hierarchical classification, where different sets of traits are examined depending on growth form. Also, at the level of interpretation, the environmental context and purpose of functional classifications need to be specified explicitly, so that global generalizations can be made by comparing across environments functional classifications derived from similar methodologies.},
-author = {Lavorel, Sandra and McIntyre, S. and Landsberg, J. and Forbes, T. D. A.},
-doi = {10.1016/S0169-5347(97)01219-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lavorel et al. - 1997 - Plant Functional Classifications from general groups to specific groups based on response to disturbance.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {12},
-pages = {474--478},
-title = {{Plant Functional Classifications: from general groups to specific groups based on response to disturbance}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534797012196},
-year = {1997}
-}
-@article{Getis1987,
-abstract = {A technique based on second-order methods, called second-order neighborhood analysis, is used to quantify clustering at various spatial scales. The theoretical model represents the degree of clustering in a Poisson process from the perspective of each individual point. The method is applied to point location data for a sample of ponderosa pine (Pinus ponderosa) trees, and shows that heterogeneity within the forest is clearly a function of the scale of analysis.},
-author = {Getis, Arthur and Franklin, Janet},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Getis, Franklin - 1987 - Second-order neighborhood analysis of mapped point patterns.pdf:pdf},
-journal = {Ecology},
-pages = {473--477},
-title = {{Second-order neighborhood analysis of mapped point patterns}},
-volume = {68},
-year = {1987}
-}
-@misc{Wilson1969,
-abstract = {In order to facilitate experiments on colonization, a technique was developed that permits the removal of the faunas of very small islands. The islands are covered by a tent and fumigated with methyl bromide at concentrations that are lethal to arthropods but not to the plants. Seven islands in Florida Bay, of varying distance and direction from immigrant sources, were censused exhaustively. The small size (diameter 11-18 m) and ecological simplicity of these islands, which consist solely of red mangrove trees (Rhizophora mangle) with no supratidal ground, allowed the location and identification of all resident species. The terrestrial fauna of these islands is composed almost exclusively of arboreal arthropods, with 20-50 species usually present at any given moment. Surveys of these taxa throughout the Florida Keys, with emphasis on the inhabitants of mangrove forests, were made during 1967 in order to estimate the size and composition of the @'species pool.@' The seven experimental islands were defaunated in late 1966 and early 1967, and the colonists were monitored for 17-20 man-hours every 18 days. Precautions were taken to avoid artificial introductions during the monitoring periods.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Wilson, Edward O. and Simberloff, Daniel S.},
-booktitle = {Ecology},
-doi = {10.2307/1934855},
-eprint = {arXiv:1011.1669v3},
-isbn = {00129658},
-issn = {00129658},
-number = {2},
-pages = {267},
-pmid = {25246403},
-title = {{Experimental Zoogeography of Islands: Defaunation and Monitoring Techniques}},
-url = {http://www.jstor.org/stable/1934855?origin=crossref},
-volume = {50},
-year = {1969}
-}
-@article{Ruiz2010,
-abstract = {Qualitative spatial variables are important in many fields of research. However, unlike the decades-worth of research devoted to the spatial association of quantitative variables, the exploratory analysis of spatial qualitative variables is relatively less developed. The objective of the present paper is to propose a new test ( Q ) for spatial independence. This is a simple, consistent, and powerful statistic for qualitative spatial independence that we develop using concepts from symbolic dynamics and symbolic entropy. The Q test can be used to detect, given a spatial distribution of events, patterns of spatial association of qualitative variables in a wide variety of settings. In order to enable hypothesis testing, we give a standard asymptotic distribution of an affine transformation of the symbolic entropy under the null hypothesis of independence in the spatial qualitative process. We include numerical experiments to demonstrate the finite sample behaviour of the test, and show its application by means of an empirical example that explores the spatial association of fast food establishments in the Greater Toronto Area in Canada.},
-author = {Ruiz, Manuel and L{\'{o}}pez, Fernando and P{\'{a}}ez, Antonio},
-doi = {10.1007/s10109-009-0100-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ruiz, L{\'{o}}pez, P{\'{a}}ez - 2010 - Testing for spatial association of qualitative data using symbolic dynamics.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {3},
-pages = {281--309},
-title = {{Testing for spatial association of qualitative data using symbolic dynamics}},
-url = {http://dx.doi.org/10.1007/s10109-009-0100-1},
-volume = {12},
-year = {2010}
-}
-@article{Combes2004a,
-abstract = {We study the impact of local economic structure on employment dynamics. Local employment is decomposed into the product of the average plant size and the number of plants in the area and industry. We estimate the dynamics of both components simultaneously using French yearly data on 36 industries and 341 areas between 1984 and 1993. The careful specification of short-run dynamics and the control for fixed effects and endogeneity are shown to be critical in the empirical model. First, static externalities are prevalent compared to dynamic ones. Moreover, whereas area-and-industry effects explain most of the spatial variation of plant size, the local number of plants is mainly driven by the current local economic structure. Policies targeted towards plant creation should thus be more efficient. For instance, large areas endowed with a small number of even size industries have both more and larger plants. A large number of plants heterogeneous in size also increases the average plant size, but the number of plants is higher when plants have similar size.},
-author = {Combes, Pierre-Philippe and Magnac, Thierry and Robin, Jean-Marc},
-doi = {10.1016/j.jue.2004.03.009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Combes, Magnac, Robin - 2004 - The Dynamics of Local Employment in France.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {2},
-pages = {217--243},
-title = {{The Dynamics of Local Employment in France}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119004000427},
-volume = {56},
-year = {2004}
-}
-@article{Smith1984,
-author = {Smith, Eric P. and Belle, Gerald Van},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith, Belle - 1984 - Nonparametric Estimation of Species Richness.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {119--129},
-title = {{Nonparametric Estimation of Species Richness}},
-volume = {40},
-year = {1984}
-}
-@article{Smith2014,
-archivePrefix = {arXiv},
-arxivId = {arXiv:1410.8082v1},
-author = {Smith, Reginald D.},
-eprint = {arXiv:1410.8082v1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith - 2014 - Malware Ecology Viewed as Ecological Succession Historical Trends and Future Prospects.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Malware "Ecology" Viewed as Ecological Succession: Historical Trends and Future Prospects}},
-volume = {1410.8082},
-year = {2014}
-}
-@article{Rao1964,
-abstract = {The paper provides various interpretations of principal components in the analysis of multiple measurements. A number of generalizations of principal components have been made specially in the study of a set of variables in relation to another set known as instrumental variables. The use of generalized principal components in applied research has been indicated. Finally, the difference between factor analysis and principal component analysis has been explained.},
-author = {Rao, C. Radhakrishna},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rao - 1964 - The Use and Interpretation of Principal Component Analysis in Applied Research.pdf:pdf},
-journal = {Sankhyā: The Indian Journal of Statistics},
-number = {4},
-pages = {329--358},
-title = {{The Use and Interpretation of Principal Component Analysis in Applied Research}},
-url = {https://www.jstor.org/stable/25049339},
-volume = {26},
-year = {1964}
-}
-@article{Ricotta2015c,
-abstract = {Aims: Presence/absence coefficients of (dis)similarity are generally based on various combinations of thematching/mismatching components of the classical 2 9 2 contingency table. While a few extensions of the contingency table to species abundance data were proposed, a generalization of such coefficients that includes species resemblances is still lacking. Methods: In this paperwe introduce a newfamily of plot-to-plot (dis)similarity coefficients, which include species abundances and interspecies resemblances in the calculation of the matching/mismatching components of the contingency table. Within this family, the behaviour of five similarity coefficients is examined by graphical comparisons based on simulated data. Conclusions: This new family of similarity coefficients can equally apply to functional or phylogenetic resemblance among species, thus providing a unified framework for comparing species turnover among plots.},
-author = {Ricotta, Carlo and Pavoine, Sandrine},
-doi = {10.1111/jvs.12329},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Pavoine - 2015 - Measuring similarity among plots including similarity among species an extension of traditional approaches.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {1061--1067},
-title = {{Measuring similarity among plots including similarity among species: an extension of traditional approaches}},
-url = {http://doi.wiley.com/10.1111/jvs.12329},
-volume = {26},
-year = {2015}
-}
-@article{Feser2002c,
-abstract = {We use the Getis/Ord local G statistic and detailed county-level industry employment data from the U.S. Bureau of Labor Statistics to isolate discrete industrial complexes–or groups of linked industries clustered in space–for two recent years: 1989 and 1997. We describe the characteristics of the complexes in terms of number, spatial extent, broad regional distribution, and other factors. Data from the two periods help illustrate key shifts in industrial locations, including the continuing concentration of the apparel industry in the Southeast and the ongoing southern shift in U.S. vehicle production. The paper builds on earlier work by Czamanski (1974), Roepke et al. (1974), Bergsman et al. (1975) and others that still has considerable relevance for the most recent research on industry clusters and geographic concentration.},
-author = {Feser, Edward J. and Sweeney, Stuart H. and Renski, H.},
-doi = {10.1111/j.0022-4146.2005.00376.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser, Sweeney, Renski - 2002 - A descriptive analysis of discrete U.S. industrial complexes.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {2},
-pages = {395--419},
-title = {{A descriptive analysis of discrete U.S. industrial complexes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0022-4146.2005.00376.x/abstract},
-volume = {45},
-year = {2005}
-}
-@techreport{Gillet2000,
-address = {Neuch{\^{a}}tel},
-author = {Gillet, Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gillet - 2000 - La phytosociologie synusiale int{\'{e}}gr{\'{e}}e. Guide m{\'{e}}thodologique.pdf:pdf},
-institution = {Universit{\'{e}} de Neuch{\^{a}}tel},
-pages = {1--68},
-title = {{La phytosociologie synusiale int{\'{e}}gr{\'{e}}e. Guide m{\'{e}}thodologique}},
-year = {2000}
-}
-@article{Rull2011,
-abstract = {The origin of extant neotropical biodiversity has been a controversial topic since the time of Darwin. In this review, I discuss the timing of, and potential driving factors associated with, diversification using recent evidence from molecular phylogenetics. Although these studies provide new insights into the subject, they are sensitive to dating approaches and targets, and can eventually lead to biased conclusions. A careful analysis suggests that the origin of extant neotropical biodiversity cannot be attributed to the action of one or few events during key time intervals. Rather, it is the result of complex ecological and evolutionary trends initiated by Neogene tectonic events and palaeogeographical reorganisations, and maintained by the action of Pleistocene climatic changes. {\textcopyright} 2011 Elsevier Ltd.},
-author = {Rull, Valent{\'{i}}},
-doi = {10.1016/j.tree.2011.05.011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rull - 2011 - Neotropical biodiversity Timing and potential drivers.pdf:pdf},
-journal = {Trends in Ecology and Evolution},
-number = {10},
-pages = {508--513},
-title = {{Neotropical biodiversity: Timing and potential drivers}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534711001443},
-volume = {26},
-year = {2011}
-}
-@article{DiGiacinto2011,
-abstract = {We propose two model-based measures of the intensity of local and global agglomeration patterns at the industry level. Spatial plant dispersion in a given industry is modeled as the outcome of an error components process that provides a convenient framework for the simultaneous treatment of strictly localized and distance-related agglomeration forces. Having dealt with maximum likelihood inference on model parameters, tackling also the issue of data censoring, the methodology is subsequently implemented on Italian census data for both manufacturing and service industries and a comparison of findings with respect to standard agglomeration and spatial autocorrelation measures is undertaken. (C) 2011 Elsevier B.V. All rights reserved.},
-annote = {ISI Document Delivery No.: 753IK
-Di Giacinto, Valter Pagnini, Marcello
-ELSEVIER SCIENCE BV},
-author = {{Di Giacinto}, V. and Pagnini, M.},
-doi = {10.1016/j.regsciurbeco.2011.01.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Di Giacinto, Pagnini - 2011 - Local and global agglomeration patterns Two econometrics-based indicators.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {3},
-pages = {266--280},
-title = {{Local and global agglomeration patterns: Two econometrics-based indicators}},
-volume = {41},
-year = {2011}
-}
-@article{Debski2002,
-abstract = {Theories accounting for the maintenance of high tree diversity in tropical rain forests range from those proposing that tropical trees are highly co-evolved niche specialists, to those proposing that they are mostly generalist, undergoing random drift. We test these hypotheses at a meaningful, community-wide scale using data on the spatial patterns and habitat preferences of all species of Aporosa (Euphorbiaceae) growing on two large rain forest plots in Malaysia. Second-order spatial pattern analyses using a method based on Ripley's K function showed that Aporosa species formed spatially distinct assemblages, and a randomization procedure suggested that these assemblages were explained by biases in their distributions in relation to habitat types. Soil type, as determined by parent material, was an important determinant of habitat preferences, although topography and forest structure also accounted for some variation. We conclude that niche differentiation is an important mechanism contributing to the coexistence of Aporosa species at the community scale. However, spatial separation due to these differential habitat biases accounted for only a portion of the high species richness observed in this genus, so other mechanisms must also be sought to account fully for the maintenance of tropical tree species richness.},
-annote = {Article
-English
-ECOLOGY
-571LD},
-author = {Debski, Igor and Burslem, David F. R. P. and Palmiotto, Peter A. and Lafrankie, James V. and Lee, Hua-Seng and Manokaran, N.},
-doi = {10.1890/0012-9658(2002)083[2005:HPOAIT]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Debski et al. - 2002 - Habitat preferences of Aporosa in two Malaysian forests Implications for abundance and coexistence.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {2005--2018},
-title = {{Habitat preferences of Aporosa in two Malaysian forests: Implications for abundance and coexistence}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282002{\%}29083[2005:HPOAIT]2.0.CO;2/abstract},
-volume = {83},
-year = {2002}
-}
-@article{Lortie1996,
-abstract = {Adaptive plasticity in plants is commonly interpreted for fitness estimates like size and fecundity. The specialization hypothesis, however, predicts that plasticity in such characters is not a product of selection but, rather, a product of specialized (i.e., ecotypic) adaptation to particular environmental conditions. In response to a recent test of this hypothesis (Emery et a!. 1994 ), we refine its predictions to recognize that the evolution of specialized ecotypes may be accompanied by an increase, decrease, or no change in the plasticity of size or fecundity. These predictions depend on whether specialization is associated with the less favorable or more favorable end of an environmental gradient and on whether specialization to one end of the gradient comes at a cost of reduced performance at the other end. We argue that, for size or fecundity characters, a plastic response to environmental deterioration is adaptive only if the alternative is dormancy or death and is generally less adaptive than phenotypic stability. Based on analysis of reaction norms for reciprocal transplants, we illustrate how it is possible to reject the specialization hypothesis and how to recognize results that are consistent with this hypothesis.},
-author = {Lortie, Christopher J. and Aarssen, Lonnie W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lortie, Aarssen - 1996 - The Specialization Hypothesis for Phenotypic Plasticity in Plants.pdf:pdf},
-journal = {International Journal of Plant Sciences},
-number = {4},
-pages = {484--487},
-title = {{The Specialization Hypothesis for Phenotypic Plasticity in Plants}},
-url = {https://www.jstor.org/stable/2475252},
-volume = {157},
-year = {1996}
-}
-@book{Halle1970,
-address = {Paris},
-author = {Hall{\'{e}}, Francis and Oldeman, Roelof A. A.},
-publisher = {Masson},
-title = {{Essai sur l'architecture et la dynamique de croissance des arbres tropicaux}},
-year = {1970}
-}
-@article{Rajala2012,
-abstract = {While much research in ecology has focused on spatially explicit modelling as well as on measures of biodiversity, the concept of spatial (or local) biodiversity has been discussed very little. This paper generalises existing measures of spatial biodiversity and introduces a family of spatial biodiversity measures by flexibly defining the notion of the individuals' neighbourhood within the framework of graphs associated to a spatial point pattern. We consider two non-independent aspects of spatial biodiversity, scattering, i.e. the spatial arrangement of the individuals in the study area and exposure, the local diversity in an individual's neighbourhood. A simulation study reveals that measures based on the most commonly used neighbourhood defined by the geometric graph do not distinguish well between scattering and exposure. This problem is much less pronounced when other graphs are used. In an analysis of the spatial diversity in a rainforest, the results based on the geometric graph have been shown to spuriously indicate a decrease in spatial biodiversity when no such trend was detected by the other types of neighbourhoods. We also show that the choice of neighbourhood markedly impacts on the classification of species according to how strongly and in what way different species spatially structure species diversity. Clearly, in an analysis of spatial or local diversity an appropriate choice of local neighbourhood is crucial in particular in terms of the biological interpretation of the results. Due to its general definition, the approach discussed here offers the necessary flexibility that allows suitable and varying neighbourhood structures to be chosen.},
-annote = {ISI Document Delivery No.: 042UK
-Times Cited: 0
-Cited Reference Count: 46
-Rajala, Tuomas Illian, Janine
-Finnish graduate school of Computations and Mathematical Sciences (COMAS); Finnish Academy of Science and Letters; Academy of Finland [111156]; National Science Foundation [DEB-0640386, DEB-0425651, DEB-034 6488, DEB-012 9874, DEB-00753102, DEB-9909347, DEB-961 5226, DEB-940 5933, DEB-922 1033, DEB-9100058, DEB-8906869, DEB-8605042, DEB-8206992, DEB-7922197]; Center for Tropical Forest Science; Smithsonian Tropical Research Institute; John D. and Catherine T. MacArthur Foundation; Mellon Foundation; Celera Foundation
-The research was funded by the Finnish graduate school of Computations and Mathematical Sciences (COMAS), a grand from the Finnish Academy of Science and Letters and Academy of Finland (project No. 111156). The authors would like to thank A. Penttinen for helpful comments and the supervision of the research. The BCI forest dynamics research project was made possible by National Science Foundation grants to Stephen P. Hubbell: DEB-0640386, DEB-0425651, DEB-034 6488, DEB-012 9874, DEB-00753102, DEB-9909347, DEB-961 5226, DEB-961 5226, DEB-940 5933, DEB-922 1033, DEB-9100058, DEB-8906869, DEB-8605042, DEB-8206992, DEB-7922197, support from the Center for Tropical Forest Science, the Smithsonian Tropical Research Institute, the John D. and Catherine T. MacArthur Foundation, the Mellon Foundation, the Celera Foundation, and numerous private individuals, and through the hard work of over 100 people from 10 countries over the past two decades. The plot project is part the Center for Tropical Forest Science, a global network of large-scale demographic tree plots.
-Springer
-Dordrecht},
-author = {Rajala, T. and Illian, J.},
-doi = {10.1007/s10651-012-0200-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rajala, Illian - 2012 - A family of spatial biodiversity measures based on graphs.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {4},
-pages = {545--572},
-title = {{A family of spatial biodiversity measures based on graphs}},
-volume = {19},
-year = {2012}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2004a,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n°84-431 du 6 juin 1984 fixant les dispositions statutaires communes applicables aux enseignants-chercheurs et portant statut particulier du corps des professeurs des universit{\'{e}}s et du corps des ma{\^{i}}tres de conf{\'{e}}rences.}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000520453},
-year = {2004}
-}
-@article{Roggy1999a,
-abstract = {The natural 15N abundance method for estimating symbiotic biological N2-fixation was tested on legume trees from two rain forests on contrasting soils (oxisols and spodosols) in French Guiana. When possible, the significance of N2-fixing species in the plant community was evaluated in terms of density, biomass and contribution of N2-fixation to the building up of the total nitrogen mass in the leaves. Of the two sites, the rain forest on spodosols was the less favourable for application of the $\delta$15N method: the available soil nitrogen was isotopically similar to fixed-N2. Hence, the results showed that a reliable estimate of N2-fixation could not be obtained. A substantial contribution of fixed-N2 to the nitrogen nutrition of legumes was found on oxisols, with an average value of 54{\%} Ndfa (Nitrogen derived from the atmosphere). The contribution of the N2-fixing legumes to the biomass of the stand was estimated to be 2 t ha-1 for the leaf biomass and 136 t ha-1 for the total above-ground plant biomass. With 7.5{\%} of trees in the stand able to fix N2 (462 out of 6156), N2-fixation was estimated to be 7 kg ha-1 y-1. These results are the first use of the $\delta$15N method to estimate nitrogen input by N2-fixing legumes to a natural rain forest. The inter-site variability observed in the $\delta$15N of the non-fixing plants suggested different nitrogen-cycling processes in the two soils. The $\delta$15N of the non-N2-fixing plants could be related to the soil nitrogen availability and be used as an indicator of efficient or non-efficient nitrogen-cycling rain forests. The spatial variability of the $\delta$15N in the plant-available soil nitrogen pool and the nitrogen balance in tropical rain forests are discussed.},
-author = {Roggy, Jean-Christophe and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise and Garbaye, Jean and Domenach, Anne-Marie},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roggy et al. - 1999 - Nitrogen cycling in the tropical rain forest of french Guiana comparison of two sites with contrasting soil types.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {1},
-pages = {1--22},
-title = {{Nitrogen cycling in the tropical rain forest of french Guiana: comparison of two sites with contrasting soil types using delta15N}},
-url = {http://www.jstor.org/stable/2560194},
-volume = {15},
-year = {1999}
-}
-@article{Lacustre2004,
-abstract = {Spatial structures may not only result from ecological interactions, they may also play an essential functional role in organizing the interactions. Modeling spatial patterns at multiple spatial and temporal scales is thus a crucial step to understand the functioning of ecological communities. PCNM (principal coordinates of neighbor matrices) analysis achieves a spectral decomposition of the spatial relationships among the sampling sites, creating variables that correspond to all the spatial scales that can be perceived in a given data set. The analysis then finds the scales to which a data table of interest responds. The significant PCNM variables can be directly interpreted in terms of spatial scales, or included in a procedure of variation decomposition with respect to spatial and environmental components. This paper presents four applications of PCNM analysis to ecological data representing combinations of: transect or surface data, regular or irregular sampling schemes, univariate or multivariate data. The data sets include Amazonian ferns, tropical marine zooplankton, chlorophyll in a marine lagoon, and oribatid mites in a peat bog. In each case, new ecological knowledge was obtained through PCNM analysis.},
-author = {Borcard, Daniel and Legendre, Pierre and Avois-Jacquet, Carol and Tuomisto, Hanna},
-doi = {10.1890/03-3111},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borcard et al. - 2004 - Dissecting the Spatial Structure of Ecological Data at Multiple Scales.pdf:pdf},
-journal = {Ecology},
-month = {jul},
-number = {7},
-pages = {1826--1832},
-title = {{Dissecting the Spatial Structure of Ecological Data at Multiple Scales}},
-url = {http://doi.wiley.com/10.1890/03-3111},
-volume = {85},
-year = {2004}
-}
-@book{R,
-address = {Vienna, Austria},
-author = {{R Core Team}},
-isbn = {3-900051-07-0},
-publisher = {R Foundation for Statistical Computing},
-title = {{R: A Language and Environment for Statistical Computing}},
-url = {http://www.r-project.org},
-year = {2017}
-}
-@article{Stein2014,
-abstract = {Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.},
-author = {Stein, Anke and Gerstner, Katharina and Kreft, Holger},
-doi = {10.1111/ele.12277},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stein, Gerstner, Kreft - 2014 - Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial sc.pdf:pdf},
-journal = {Ecology Letters},
-number = {7},
-pages = {866--880},
-title = {{Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12277/abstract},
-volume = {17},
-year = {2014}
-}
-@article{Volkov2003,
-abstract = {The theory of island biogeography(1) asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell(2) generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity(2) and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions(3), we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama(4), than the lognormal distribution(5,6).},
-annote = {ISI Document Delivery No.: 715QR
-Times Cited: 243
-Cited Reference Count: 28
-Volkov, I Banavar, JR Hubbell, SP Maritan, A
-Nature publishing group
-London},
-author = {Volkov, Igor and Banavar, Jayanth R. and Hubbell, Stephen P. and Maritan, Amos},
-doi = {10.1038/nature01883},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Volkov et al. - 2003 - Neutral theory and relative species abundance in ecology.pdf:pdf},
-journal = {Nature},
-number = {6952},
-pages = {1035--1037},
-title = {{Neutral theory and relative species abundance in ecology}},
-url = {http://www.nature.com/nature/journal/v424/n6952/abs/nature01883.html},
-volume = {424},
-year = {2003}
-}
-@article{Haegeman2010,
-abstract = {Entropy maximization (EM, also known as MaxEnt) is a general inference procedure that originated in statistical mechanics. It has been applied recently to predict ecological patterns, such as species abundance distributions and species-area relationships. It is well known in physics that the EM result strongly depends on how elementary configurations are described. Herewe argue that the same issue is also of crucial importance for EM applications in ecology. To illustrate this, we focus on the EM prediction of species-level spatial abundance distributions. We show that the EM outcome de- pends on (1) the choice of configuration set, (2) the way constraints are imposed, and (3) the scale on which the EM procedure is applied. By varying these choices in the EM model, we obtain a large range of EM predictions. Interestingly, they correspond to spatial abun- dance distributions that have been derived previously from mech- anistic models.We argue that the appropriate choice of theEMmodel assumptions is nontrivial and can be determined only by comparison with empirical data},
-author = {Haegeman, Bart and Etienne, Rampal S.},
-doi = {doi:10.1086/650718},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haegeman, Etienne - 2010 - Entropy Maximization and the Spatial Distribution of Species.pdf:pdf},
-journal = {The American Naturalist},
-number = {4},
-pages = {E74--E90},
-title = {{Entropy Maximization and the Spatial Distribution of Species}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/650718},
-volume = {175},
-year = {2010}
-}
-@article{Dray2012,
-abstract = {Species spatial distributions are the result of population demography, behavioral traits, and species interactions in spatially heterogeneous environmental conditions. Hence the composition of species assemblages is an integrative response variable, and its variability can be explained by the complex interplay among several structuring factors. The thorough analysis of spatial variation in species assemblages may help infer processes shaping ecological communities. We suggest that ecological studies would benefit from the combined use of the classical statistical models of community composition data, such as constrained or unconstrained multivariate analyses of site-by-species abundance tables, with rapidly emerging and diversifying methods of spatial pattern analysis. Doing so allows one to deal with spatially explicit ecological models of beta diversity in a biogeographic context through the multiscale analysis of spatial patterns in original species data tables, including spatial characterization of fitted or residual variation from environmental models. We summarize here the recent progress for specifying spatial features through spatial weighting matrices and spatial eigenfunctions in order to define spatially constrained or scale-explicit multivariate analyses. Through a worked example on tropical tree communities, we also show the potential of the overall approach to identify significant residual spatial patterns that could arise from the omission of important unmeasured explanatory variables or processes.},
-annote = {ISI Document Delivery No.: 999YN
-Times Cited: 0
-Cited Reference Count: 123
-Dray, S. Pelissier, R. Couteron, P. Fortin, M. -J. Legendre, P. Peres-Neto, P. R. Bellier, E. Bivand, R. Blanchet, F. G. De Caceres, M. Dufour, A. -B. Heegaard, E. Jombart, T. Munoz, F. Oksanen, J. Thioulouse, J. Wagner, H. H.
-University Lyon 1; PRABI; LBBE; UMR CNRS [5558]; NSERC Discovery Grants; [ANR 07 BDIV 014-03]
-This contribution originated from the SEDAR workshop partially funded by the University Lyon 1, the PRABI, and the LBBE, UMR CNRS 5558. This research was supported by grants ANR 07 BDIV 014-03 to S. Dray, NSERC Discovery Grants to M. J. Fortin, P. Legendre, P. Peres-Neto, and H. H. Wagner, MEDD 05 EcoTrop (OSDA) 0000223 to R. Pelissier, P. Couteron, and F. Munoz, and a Canada Research Chair to P. Peres-Neto. F. G. Blanchet was supported by an NSERC Discovery Grant to Fangliang He. We thank Carsten Dormann and two anonymous reviewers for comments on an earlier version of the manuscript. Stephane Dray, Raphael Pelissier, Pierre Couteron, Marie-Josee Fortin, Pierre Legendre, and Pedro R. Peres-Neto contributed equally to this work.
-Ecological soc amer
-Washington},
-author = {Dray, St{\'{e}}phane and P{\'{e}}lissier, Rapha{\"{e}}l and Couteron, Pierre and Fortin, Marie-Jos{\'{e}}e and Legendre, Pierre and Peres-Neto, Pedro R. and Bellier, E. and Bivand, Roger and Blanchet, F. Guillaume and {De Caceres}, M. and Dufour, Anne-B{\'{e}}atrice and Heegaard, E. and Jombart, T. and Munoz, Fran{\c{c}}ois and Oksanen, Jari and Thioulouse, Jean and Wagner, Helene H.},
-doi = {10.1890/11-1183.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dray et al. - 2012 - Community ecology in the age of multivariate multiscale spatial analysis.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {257--275},
-title = {{Community ecology in the age of multivariate multiscale spatial analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/11-1183.1/abstract},
-volume = {82},
-year = {2012}
-}
-@article{Tamas2001,
-abstract = {Alternative community analyses, based on quantitative and presence/absence data, are comparable logically if the data type is the only factor responsible for differences among results. For presence/absence indices that consider mutual absences, no quantitative alternatives are known. To facilitate such comparisons, a new family of similarity coefficients is proposed for abundance data. Formally, this extension is achieved by generalizing the four cells of the usual 2 × 2 contingency table to the quantitative case. This implies an expanded meaning of absence: for a given species at a given site it is understood as the difference between the actual value and the maximum detected in the entire study. The correspondence between 10 presence/absence coefficients and their quantitative counterparts is evaluated by graphical compari- sons based on artificial data. The behaviour of the new func- tions is also examined using field data representing post-fire regeneration processes in grasslands and a chronosequence pertaining to forest regeneration after clear-cut. The examples suggest that the new coefficients are most informative for data sets with low beta-diversity and temporal background changes.},
-author = {Tam{\'{a}}s, Jlia and Podani, J{\'{a}}nos and Csontos, P{\'{e}}ter},
-doi = {10.2307/3236854},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tam{\'{a}}s, Podani, Csontos - 2001 - An extension of presenceabsence coefficients to abundance data a new look at absence.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {401--410},
-title = {{An extension of presence/absence coefficients to abundance data: a new look at absence}},
-volume = {12},
-year = {2001}
-}
-@article{Atkinson1970,
-author = {Atkinson, Anthony B},
-doi = {10.1016/0022-0531(70)90039-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Atkinson - 1970 - On the measurement of inequality.pdf:pdf},
-issn = {00220531},
-journal = {Journal of Economic Theory},
-month = {sep},
-number = {3},
-pages = {244--263},
-title = {{On the measurement of inequality}},
-url = {https://www.sciencedirect.com/science/article/pii/0022053170900396},
-volume = {2},
-year = {1970}
-}
-@article{Wang2005,
-abstract = {BACKGROUND:In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experimental design, as well as clues to the diversity of expressed genes in the tissue from which the library was constructed. RESULTS:We propose a compound Poisson process model that can accurately predict the gene capture in a future EST sample based on an initial EST sample. It also allows estimation of the number of expressed genes in one cDNA library or co-expressed in two cDNA libraries. The superior performance of the new prediction method over an existing approach is established by a simulation study. Our analysis of four Arabidopsis thaliana EST sets suggests that the number of expressed genes present in four different cDNA libraries of Arabidopsis thaliana varies from 9155 (root) to 12005 (silique). An observed fraction of co-expressed genes in two different EST sets as low as 25{\%} can correspond to an actual overlap fraction greater than 65{\%}. CONCLUSION:The proposed method provides a convenient tool for gene capture prediction and cDNA library property diagnosis in EST sequencing.},
-author = {Wang, Ji-Ping and Lindsay, Bruce and Cui, Liying and Wall, P. Kerr and Marion, Josh and Zhang, Jiaxuan and DePamphilis, Claude},
-doi = {10.1186/1471-2105-6-300},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wang et al. - 2005 - Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries.pdf:pdf},
-journal = {BMC Bioinformatics},
-number = {1},
-pages = {300},
-title = {{Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries}},
-url = {http://www.biomedcentral.com/1471-2105/6/300},
-volume = {6},
-year = {2005}
-}
-@article{Montgomery2001,
-abstract = {Large-scale topographic analyses show that hemisphere-scale climate$\backslash$nvariations are a first-order control on the morphology of the Andes.$\backslash$nZonal atmospheric circulation in the Southern Hemisphere creates$\backslash$nstrong latitudinal precipitation gradients that, when incorporated$\backslash$nin a generalized index of erosion intensity, predict strong gradients$\backslash$nin erosion rates both along and across the Andes. Cross-range asymmetry,$\backslash$nwidth, hypsometry, and maximum elevation reflect gradients in both$\backslash$nthe erosion index and the relative dominance of fluvial, glacial,$\backslash$nand tectonic processes, and show that major morphologic features$\backslash$ncorrelate with climatic regimes. Latitudinal gradients in inferred$\backslash$ncrustal thickening and structural shortening correspond to variations$\backslash$nin predicted erosion potential, indicating that, like tectonics,$\backslash$nnonuniform erosion due to large-scale climate patterns is a first-order$\backslash$ncontrol on the topographic evolution of the Andes.},
-author = {Montgomery, David R. and Balco, Greg and Willett, Sean D.},
-doi = {10.1130/0091-7613(2001)029<0579:CTATMO>2.0.CO;2},
-journal = {Geology},
-number = {7},
-pages = {579--582},
-title = {{Climate, tectonics, and the morphology of the Andes}},
-volume = {29},
-year = {2001}
-}
-@article{Tilman2001,
-abstract = {Plant diversity and niche complementarity had progressively stronger effects on ecosystem functioning during a 7-year experiment, with 16-species plots attaining 2.7 times greater biomass than monocultures. Diversity effects were neither transients nor explained solely by a few productive or unviable species. Rather, many higher-diversity plots outperformed the best monoculture. These results help resolve debate over biodiversity and ecosystem functioning, show effects at higher than expected diversity levels, and demonstrate, for these ecosystems, that even the best-chosen monocultures cannot achieve greater productivity or carbon stores than higher-diversity sites.},
-author = {Tilman, David and Reich, Peter B. and Knops, Johannes and Wedin, David and Mielke, T. and Lehman, Clarence},
-doi = {10.1126/science.1060391},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tilman et al. - 2001 - Diversity and productivity in a long-term grassland experiment.pdf:pdf},
-journal = {Science},
-number = {5543},
-pages = {843--845},
-title = {{Diversity and productivity in a long-term grassland experiment}},
-url = {http://science.sciencemag.org/content/294/5543/843},
-volume = {294},
-year = {2001}
-}
-@book{Clements1916a,
-abstract = {This is a reproduction of a library book that was digitized by Google as part of an ongoing effort to preserve the information in books and make it universally accessible. http://books.google.com},
-author = {Clements, Frederic E.},
-booktitle = {Carnegie Institution of Washington},
-isbn = {3663537137},
-pages = {512},
-title = {{Plant Succession}},
-year = {1916}
-}
-@article{Ciccone1996,
-abstract = {To explain the large differences in labor productivity across U.S. states we es- timate two models-one based on local geographical externalities and the other on the diversity of local intermediate services-where spatial density results in aggregate increasing returns. Both models lead to a relation between county employment density and productivity at the state level. Using data on gross state output we find that a doubling of employment density increases average labor productivity by around 6 percent. More than half of the variance of output per worker across states can be explained by differences in the density of economic activity.},
-author = {Ciccone, Antonio and Hall, Robert E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ciccone, Hall - 1996 - Productivity and the Density of Economic Activity.pdf:pdf},
-journal = {The American Economic Review},
-number = {1},
-pages = {54--70},
-title = {{Productivity and the Density of Economic Activity}},
-url = {http://www.jstor.org/stable/2118255},
-volume = {86},
-year = {1996}
-}
-@article{Chase2014,
-abstract = {The 50-ha long-term forest plot on Barro Colorado Island in Panama was `ground zero' for the development of ecology's `neutral theory' and comparisons with its `niche theory' counterpart. In this issue, Garzon-Lopez and colleagues used tree distributions at this site to recast the unresolved (and unresolvable) debate to show that observational scale drives the perception of which processes predominate.},
-author = {Chase, Jonathan M.},
-doi = {10.1111/jvs.12159},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chase - 2014 - Spatial scale resolves the niche versus neutral theory debate.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {319--322},
-title = {{Spatial scale resolves the niche versus neutral theory debate}},
-url = {http://doi.wiley.com/10.1111/jvs.12159},
-volume = {25},
-year = {2014}
-}
-@article{Brown2002,
-abstract = {Underlying the diversity of life and the complexity of ecology is order that reflects the operation of fundamental physical and biological processes. Power laws describe empirical scaling relationships that are emergent quantitative features of biodiversity. These features are patterns of structure or dynamics that are self-similar or fractal-like over many orders of magnitude. Power laws allow extrapolation and prediction over a wide range of scales. Some appear to be universal, occurring in virtually all taxa of organisms and types of environments. They offer clues to underlying mechanisms that powerfully constrain biodiversity. We describe recent progress and future prospects for understanding the mechanisms that generate these power laws, and for explaining the diversity of species and complexity of ecosystems in terms of fundamental principles of physical and biological science.},
-author = {Brown, James H. and Gupta, Vijay K. and Li, Bai-Lian and Milne, Bruce T. and Restrepo, Carla and West, Geoffrey B.},
-doi = {10.1098/rstb.2001.0993},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brown et al. - 2002 - The fractal nature of nature power laws, ecological complexity and biodiversity.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1421},
-pages = {619--626},
-title = {{The fractal nature of nature: power laws, ecological complexity and biodiversity.}},
-url = {http://rstb.royalsocietypublishing.org/content/357/1421/619},
-volume = {357},
-year = {2002}
-}
-@article{Veron2016,
-abstract = {Background Phylogenetic diversity and evolutionary distinctiveness are highly valuable components of biodiversity, but they are rarely considered in conservation practices. Focusing on a biodiversity hotspot, the Mediterranean Basin, we aimed to identify those areas where evolutionary history is highly threatened and range-restricted in the region. Using null models, we first compared the spatial distributions of three indices: two measured threatened evolutionary history—Expected PDloss and Heightened Evolutionary distinctiveness and Global Endangerment—and one measured endemic evolutionary history—Biogeographically Evolutionary Distinctiveness. We focused on three vertebrate groups with high proportions of endemic, threatened species: amphibians, squamates and terrestrial mammals. Second, we estimated the spatial overlap of hotspots of threatened and endemic evolutionary history within the network of protected areas under several conservation scenarios. Results Areas that concentrate evolutionary history of conservation interest greatly differed among taxa and indices, although a large proportion of hotspots were identified in the Maghreb, in the East of the Mediterranean Basin as well as in islands. We found that, in a minimum conservation scenario, there was a significant proportion of hotspots for amphibians and squamates that were protected but not for terrestrial mammals. However, in a strong conservation scenario, only few hotspots overlapped with protected areas and they were significantly less protected than in a model where hotspots were chosen randomly. Conclusions Some sites concentrate highly threatened and range-restricted evolutionary history of the Mediterranean basin and their conservation could be much improved. These sites are relevant for conservation studies aimed at designing new conservation actions to preserve evolutionary history and the option values it represents.},
-author = {Veron, Simon and Clergeau, Philippe and Pavoine, Sandrine},
-doi = {10.1186/s12898-016-0099-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veron, Clergeau, Pavoine - 2016 - Loss and conservation of evolutionary history in the Mediterranean Basin.pdf:pdf},
-journal = {BMC Ecology},
-number = {1},
-pages = {43},
-title = {{Loss and conservation of evolutionary history in the Mediterranean Basin}},
-url = {http://bmcecol.biomedcentral.com/articles/10.1186/s12898-016-0099-3},
-volume = {16},
-year = {2016}
-}
-@inproceedings{Loreau2005,
-address = {Paris, France.},
-author = {Loreau, Michel},
-booktitle = {Actes de la Conf{\'{e}}rence internationale Biodiversit{\'{e}} Science et Gouvernance},
-editor = {Barbault, Robert and {Le Duc}, Jean-Patrick},
-isbn = {2856535895},
-pages = {254--256},
-publisher = {IRD Editions},
-title = {{Discours de cl{\^{o}}ture}},
-year = {2005}
-}
-@article{Plotkin2000,
-abstract = {A fundamental question in ecology is how many species occur within a given area. Despite the complexity and diversity of different ecosystems, there exists a surprisingly simple, approximate answer: the number of species is proportional to the size of the area raised to some exponent. The exponent often turns out to be roughly 1/4. This power law can be derived from assumptions about the relative abundances of species or from notions of self-similarity. Here we analyze the largest existing data set of location-mapped species: over one million, individually identified trees from five tropical forests on three continents. Although the power law is a reasonable, zeroth-order approximation of our data, we find consistent deviations from it on all spatial scales. Furthermore, tropical forests are not self-similar at areas 50 hectares. We develop an extended model of the species-area relationship, which enables us to predict large-scale species diversity from small-scale data samples more accurately than any other available method.},
-author = {Plotkin, Joshua B. and Potts, Matthew D. and Yu, Douglas W. and Bunyavejchewin, Sarayudh and Condit, Richard and Foster, Robin B. and Hubbell, Stephen P. and LaFrankie, James and Manokaran, N. and Lee, Hua-Seng and Sukumar, Raman and Nowak, Martin A. and Ashton, Peter S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Plotkin et al. - 2000 - Predicting species diversity in tropical forests.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {20},
-pages = {10850--10854},
-title = {{Predicting species diversity in tropical forests}},
-volume = {97},
-year = {2000}
-}
-@article{Nielsen2003,
-abstract = {Estimating paternity and genetic relatedness is central to many empirical and theoretical studies of social insects. The two important measures of a queen's mating number are her actual number of mates and her effective number of mates. Estimating the effective number of mates is mathematically identical to the problem of estimating the effective number of alleles in population genetics, a common measure of genetic variability introduced by Kimura {\&} Crow (1964). We derive a new bias-corrected estimator of effective number of types (mates or alleles) and compare this new method to previous methods for estimating true and effective numbers of types using Monte Carlo simulations. Our simulation results suggest that the examined estimators of the true number of types have very similar statistical properties, whereas the estimators of effective number of types have quite different statistical properties. Moreover, our new proposed estimator of effective number of types is approximately unbiased, and has considerably lower variance than the original estimator. Our new method will help researchers more accurately estimate intracolony genetic relatedness of social insects, which is an important measure in understanding their ecology and social behaviour. It should also be of use in population genetic studies in which the effective number of alleles is of interest.},
-author = {Nielsen, Rasmus and Tarpy, David R. and Reeve, H. Kern},
-doi = {10.1046/j.1365-294X.2003.01994.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nielsen, Tarpy, Reeve - 2003 - Estimating effective paternity number in social insects and the effective number of alleles in a populati.pdf:pdf},
-journal = {Molecular Ecology},
-number = {11},
-pages = {3157--3164},
-title = {{Estimating effective paternity number in social insects and the effective number of alleles in a population}},
-url = {http://dx.doi.org/10.1046/j.1365-294X.2003.01994.x},
-volume = {12},
-year = {2003}
-}
-@article{Harte1999a,
-abstract = {Vegetation census data from montane meadow plots are used to test a predicted connection between the species-area relationship, S=cAz, and the dependence of interpatch species turnover on patch area A, interpatch distance D, and the species-area exponent z. At small spatial scales, from D ≈ 1 - 10 m, where species-area parameters can be independently estimated, the prediction is confirmed; at larger scales, from D≈ 1-104 m, the scale-dependence of z is deduced. A predicted dependence of species richness on the shape of censused patches is also confirmed. Our results indicate that readily obtainable species-turnover data between distant small patches can be used to estimate species-area exponents at landscape scales where census data for nested areas are generally not available, thereby improving our ability to estimate landscape-scale species richness and rarity.},
-author = {Harte, John and Mccarthy, Sarah and Taylor, Kevin and Kinzig, Ann and Fischer, Marc L.},
-doi = {10.2307/3546568},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harte et al. - 1999 - Estimating species-area relationships from scale plot to landscape data using species spatial-turnover.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {45--54},
-title = {{Estimating species-area relationships from scale plot to landscape data using species spatial-turnover}},
-url = {https://www.jstor.org/stable/3546568},
-volume = {86},
-year = {1999}
-}
-@techreport{Thompson2009,
-author = {Thompson, Ian and Mackey, Brenda and McNulty, Steven and Mosseler, Alex},
-booktitle = {CBD Technical Series},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thompson et al. - 2009 - Forest Resilience, Biodiversity, and Climate Change. A synthesis of the biodiversityresiliencestability relatio.pdf:pdf},
-pages = {67},
-publisher = {Secretariat of the Convention on Biological Diversity},
-title = {{Forest Resilience, Biodiversity, and Climate Change. A synthesis of the biodiversity/resilience/stability relationship in Forest Ecosystems}},
-volume = {43},
-year = {2009}
-}
-@book{Felsenstein2004,
-author = {Felsenstein, Joseph},
-edition = {2nd Ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Felsenstein - 2004 - Inferring Phylogenies.pdf:pdf},
-isbn = {978-0878931774},
-publisher = {Sinauer Associates},
-title = {{Inferring Phylogenies}},
-year = {2004}
-}
-@article{Henderson1995,
-abstract = {This paper uses data for eight manufacturing industries in 1970 and 1987 to test for and characterize dynamic production externalities in cities. We find evidence of both MAR externalities, which are associated with past own industry employment concentration, and Jacobs externalities, which are associated with past diversity of local total employment. More specifically, for mature capital goods industries, there is evidence of MAR externalities but none of Jacobs externalities. For new high-tech industries, there is evidence of Jacobs and MAR externalities. These findings are consistent with notions of urban specialization and product cycles: new industries prosper in large, diverse metropolitan areas, but with maturity, production decentralizes to smaller, more specialized cities. For mature industries, there is also a high degree of persistence in individual employment patterns across cities, fostered by both MAR externalities and persistence in regional comparative advantage.},
-author = {Henderson, J. Vernon and Kuncoro, Ari and Turner, Matt},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Henderson, Kuncoro, Turner - 1995 - Industrial Development in Cities.pdf:pdf},
-journal = {Journal of Political Economy},
-number = {5},
-pages = {1067--1090},
-title = {{Industrial Development in Cities}},
-url = {https://www.jstor.org/stable/2138755},
-volume = {103},
-year = {1995}
-}
-@article{Getis1992,
-abstract = {Introduced in this paper is a family of statistics, G, that can be used as a measure of spatial association in a number of circumstances. The basic statistic is derived, its properties are identified, and its advantages explained. Several of the G statistics make it possible to evaluate the spatial association of a variable within a specified distance of a single point. A comparison is made between a general G statistic and Moran's I for similar hypothetical and empirical conditions. The empirical work includes studies of sudden infant death syndrome by county in North Carolina and dwelling unit prices in metropolitan San Diego by zip-code districts. Results indicate that G statistics should be used in conjunction with I in order to identify characteristics of patterns not revealed by the I statistic alone and, specifically, the Gi and Gi* statistics enable us to detect local “pockets” of dependence that may not show up when using global statistics.},
-author = {Getis, Arthur and Ord, J. K.},
-doi = {10.1111/j.1538-4632.1992.tb00261.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Getis, Ord - 1992 - The analysis of spatial association by use of distance statistics.pdf:pdf},
-journal = {Geographical Analysis},
-number = {3},
-pages = {189--199},
-title = {{The analysis of spatial association by use of distance statistics}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1992.tb00261.x/abstract},
-volume = {24},
-year = {1992}
-}
-@article{Buzas1996,
-abstract = {Fifty years of ecological research have failed to achieve an integrated, quantitative analysis suitable for both marine and terrestrial biodiversity. A new approach is presented that reconciles the interrelationship of the number of individuals and species with population structure. Sample size dependency, always the primary obstacle, is here recognized as the primary missing requirement for biodiversity analysis. With this key, and a new decomposition formula, two historically intractable problems are solved: (1) inability to separate species effects of richness and evenness within the same system (by the development of a decomposition formula to separate species richness (S), an information function (H), and species evenness (E)), and (2) correlation of diversity measures and non-specificity of statistical distributions with sample size (an analysis of S, H and E as a function of N, denoted a SHE analysis). In addition to providing resolution for ecological investigations, this approach reveals ordered structure in inventory and monitoring situations, undetectable by any other approach. As an example, Bolivian and Guyanan trees are shown to exhibit uniquely distinct and heretofore unseen diversity patterns.},
-author = {Buzas, Martin A. and Hayek, Lee-Ann C.},
-doi = {10.2307/2999767},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Buzas, Hayek - 1996 - Biodiversity resolution an integrated approach.pdf:pdf},
-journal = {Biodiversity Letters},
-number = {2},
-pages = {40--43},
-title = {{Biodiversity resolution: an integrated approach}},
-url = {http://www.jstor.org/stable/2999767},
-volume = {3},
-year = {1996}
-}
-@article{Petchey2003,
-abstract = {Separating the mechanisms that influence ecosystem functioning has been a goal of recent high profile experiments. Integrating the various experimental and analytical methods that attempt this goal across terrestrial and aquatic ecosystems, as well as careful definition of ‘complementarity', produces novel insights and valuable lessons about new directions for research. (1) Experimental designs differ in temporal scale and whether standing stock or another ecosystem process was the response variable. (2) Mathematically identical variables in different designs have contrasting ecological interpretations. For example, different sets of ecological processes can contribute to different variables in different experimental designs. (3) The frequency of transgres- sive overyielding of standing stock (e.g. total above ground biomass) in polycultures implies little about the prevalence of transgressive overyielding in other ecosystem processes. (4) Measuring the contribution to ecosystem functioning of individual species, rather than just total ecosystem functioning of a polyculture, is not essential for estimating effects of complementarity. (5) Further research will profit from distinguishing standing stock from all other ecosystem functions. (6) None of the analytic methods can distinguish the effects of individual processes or mechanisms such as resource use differentiation, facilitation, or allelopathy, for which additional experimental treatments are required. O.},
-annote = {Article},
-author = {Petchey, Owen L.},
-doi = {10.1034/j.1600-0706.2003.11828.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Petchey - 2003 - Integrating methods that investigate how complementarity influences ecosystem functioning.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {323--330},
-title = {{Integrating methods that investigate how complementarity influences ecosystem functioning}},
-url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2003.11828.x/abstract},
-volume = {101},
-year = {2003}
-}
-@book{Dagnelie1975,
-author = {Dagnelie, Pierre},
-publisher = {Les presses agronomiques de Gembloux},
-title = {{Analyse statistique {\`{a}} plusieurs variables}},
-year = {1975}
-}
-@article{Harte2005,
-abstract = {A theory of spatial structure in ecological communities is presented and tested. At the core of the theory is a simple allocation rule for the assembly of species in space. The theory leads, with no adjustable parameters, to nonrandorn statistical predictions for the spatial distribution of species at multiple spatial scales. The distributions are such that the abundance of a species at the largest measured scale uniquely determines the spatial-abundance distribution of the individuals of that species at smaller spatial scales. The shape of the species-area relationship, the endemics- area relationship, a scale-dependent community-level spatial-abundance distribution, the species-abundance distribution at small spatial scales, an index of intraspecific aggregation, the range- area relationship, and the dependence of species turnover on interpatch distance and on patch size are also uniquely predicted as a function solely of the list of abundances of the species at the largest spatial scale. We show that the spatial structure of three spatially explicit vegetation census data sets (i.e., a 64-m(2) serpentine grassland plot, a 50-ha moist. tropical forest plot, and a 9.68- ha dry tropical forest plot) are generally consistent with the predictions of the theory, despite the very simple statistical assumption upon which the theory is based, and the absence of adjustable parameters. However, deviations between predicted and observed distributions do arise for the species with the highest abundances; the pattern of those deviations indicates that the theory, which currently contains no explicit description of interaction mechanisms among individuals within species, could be improved with the incorporation of intraspecific density dependence.},
-author = {Harte, John and Conlisk, Erin and Ostling, Annette and Green, Jessica L. and Smith, Adam B.},
-doi = {10.1289/ehp.1002503},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harte et al. - 2005 - A Theory of Spatial Structure in Ecological Communities at Multiple Spatial Scales.pdf:pdf},
-journal = {Ecological Monographs},
-number = {2},
-pages = {179--197},
-title = {{A Theory of Spatial Structure in Ecological Communities at Multiple Spatial Scales}},
-volume = {75},
-year = {2005}
-}
-@article{Okabe2001,
-abstract = {This paper proposes two statistical methods, called the network K-function method and the network cross K-function method, for analyzing the distribution of points on a network. First, by extending the ordinary K-function method defined on a homogeneous infinite plane with the Euclidean distance, the paper formulates the K-function method and the cross K-function method on a finite irregular network with the shortest-path distance. Second, the paper shows advantages of the network K-function methods, such as that the network K-function methods can deal with spatial point processes on a street network in a small district, and that they can exactly take the boundary effect into account. Third, the paper develops the computational implementation of the network K-functions, and shows that the computational order of the K-function method is O(n(Q)(2) log n(Q)) and that of the network cross K-function is Q(n(Q) log n(Q)) where n(Q) is the number of nodes of a network.},
-annote = {Okabe, A Yamada, I},
-author = {Okabe, Atsuyuki and Yamada, Ikuho},
-doi = {10.1111/j.1538-4632.2001.tb00448.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Okabe, Yamada - 2001 - The K-function method on a network and its computational implementation.pdf:pdf},
-journal = {Geographical Analysis},
-number = {3},
-pages = {271--290},
-title = {{The K-function method on a network and its computational implementation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.2001.tb00448.x/abstract},
-volume = {33},
-year = {2001}
-}
-@article{Chiarucci2011,
-abstract = {Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.},
-author = {Chiarucci, Alessandro and Bacaro, Giovanni and Scheiner, Samuel M.},
-doi = {10.1098/rstb.2011.0065},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiarucci, Bacaro, Scheiner - 2011 - Old and new challenges in using species diversity for assessing biodiversity.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1576},
-pages = {2426--2437},
-title = {{Old and new challenges in using species diversity for assessing biodiversity}},
-volume = {366},
-year = {2011}
-}
-@article{Bryant2008,
-abstract = {The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ.},
-author = {Bryant, Jessica A. and Lamanna, Christine and Morlon, H{\'{e}}l{\`{e}}ne and Kerkhoff, Andrew J. and Enquist, Brian J. and Green, Jessica L.},
-doi = {10.1073/pnas.0801920105},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bryant et al. - 2008 - Microbes on mountainsides Contrasting elevational patterns of bacterial and plant diversity.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-pages = {11505--11511},
-title = {{Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity.}},
-volume = {105 Suppl},
-year = {2008}
-}
-@article{Plotkin2000a,
-abstract = {The relationship between species diversity and sampled area is fundamental to ecology. Traditionally, theories of the species-area relationship have been dominated by randomplacement models. Such models were used to formulate the canonical theory of species-area curves and species abundances. In this paper, however, armed with a detailed data set from a moist tropical forest, we investigate the validity of random placement and suggest improved models based upon spatial aggregation. By accounting for intraspecific, small-scale aggregation, we develop a cluster model which reproduces empirical species-area curves with high fidelity. We find that inter-specific aggregation patterns, on the other hand, do not a!ect the species-area curves significantly. We demonstrate that the tendency for a tree species to aggregate, as well as its average clump size, is not significantly correlated with the species' abundance. In addition, we investigate hierarchical clumping and the extent to which aggregation is driven by topography. We conclude that small-scale phenomena such as dispersal and gap recruitment determine individual tree placement more than adaptation to larger-scale topography.},
-author = {Plotkin, Joshua B. and Potts, Matthew D. and Leslie, Nandi and Manokaran, N. and LaFrankie, James V. and Ashton, Peter S.},
-doi = {10.1006/jtbi.2000.2158},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Plotkin et al. - 2000 - Species-area curves, spatial aggregation, and habitat specialization in tropical forests.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {1},
-pages = {81--99},
-title = {{Species-area curves, spatial aggregation, and habitat specialization in tropical forests}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519300921581},
-volume = {207},
-year = {2000}
-}
-@article{Arje2016,
-abstract = {The percent model affinity (PMA) index is used to measure the similarity of two probability profiles representing, for example, an ideal profile (i.e. reference condition) and a monitored profile (i.e. possibly impacted condition). The goal of this work is to study the effects of sample size, evenness, true value of the index and number of classes on the statistical properties of the estimator of the PMA index. We derive and extend previous formulas of the expectation and variance of the estimator for estimated monitored profile and fixed reference profile. Using the obtained extension, we find that the estimator is asymptotically unbiased, converging faster when the profiles differ. When both profiles are estimated, we calculate the expectation using transformation rules for expectation and in addition derive the formula for the estimator's variance. Since the computation of the probabilities in the variance formula is slow, we study the behavior of the variance with simulation experiments and assess whether it could be approximated with the variance for the fixed reference profile. Finally, we provide a set of recommendations for the users of the PMA index to avoid the most common caveats of the index.},
-author = {{\"{A}}rje, Johanna and Choi, Kwok-Pui and Divino, Fabio and Meissner, Kristian and K{\"{a}}rkk{\"{a}}inen, Salme},
-doi = {10.1007/s00477-015-1202-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/{\"{A}}rje et al. - 2016 - Understanding the statistical properties of the percent model affinity index can improve biomonitoring related deci.pdf:pdf},
-journal = {Stochastic Environmental Research and Risk Assessment},
-number = {7},
-pages = {1981--2008},
-title = {{Understanding the statistical properties of the percent model affinity index can improve biomonitoring related decision making}},
-url = {http://link.springer.com/10.1007/s00477-015-1202-6},
-volume = {30},
-year = {2016}
-}
-@book{Lindsay2011,
-author = {Lindsay, David},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lindsay - 2011 - Scientific Writing =Thinking in Words.pdf:pdf},
-isbn = {0643100466,9780643100466},
-publisher = {CSIRO Publishing},
-title = {{Scientific Writing =Thinking in Words}},
-year = {2011}
-}
-@article{Duranton2008,
-abstract = {We use a point-pattern methodology to explore the de- tailed location patterns of UK manufacturing industries. In particular, we consider the location of entrants and exiters vs. continuing estab- lishments, domestic- vs. foreign-owned, large vs. small, and affiliated vs. independent. We also examine co-localisation between vertically- linked industries. Our analysis provides a set of new stylised facts and confirmation for others.},
-author = {Duranton, Gilles and Overman, Henry G.},
-doi = {10.1111/j.1365-2966.2006.0547.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton, Overman - 2008 - Exploring the Detailed Location Patterns of UK Manufacturing Industries using Microgeographic Data.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {1},
-pages = {213--243},
-title = {{Exploring the Detailed Location Patterns of UK Manufacturing Industries using Microgeographic Data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2006.0547.x/abstract},
-volume = {48},
-year = {2008}
-}
-@article{Chao2013,
-abstract = {Estimating Shannon entropy and its exponential from incomplete samples is a central objective of many research fields. However, empirical estimates of Shannon entropy and its exponential depend strongly on sample size and typically exhibit substantial bias. This work uses a novel method to obtain an accurate, low-bias analytic estimator of entropy, based on species frequency counts. Our estimator does not require prior knowledge of the number of species. * We show that there is a close relationship between Shannon entropy and the species accumulation curve, which depicts the cumulative number of observed species as a function of sample size. We reformulate entropy in terms of the expected discovery rates of new species with respect to sample size, i.e., the successive slopes of the species accumulation curve. Our estimator is obtained by applying slope estimators derived from an improved Good-Turing frequency formula. Our method is also applied to estimate mutual information. * Extensive simulations from theoretical models and real surveys show that if sample size is not unreasonably small the resulting entropy estimator is nearly unbiased. Our estimator generally outperforms all previous methods in terms of bias and accuracy (low mean squared error) especially when species richness is large and there is a large fraction of undetected species in samples. * We discuss the extension of our approach to estimate Shannon entropy for multiple incidence data. The use of our estimator in constructing an integrated rarefaction and extrapolation curve of entropy (or mutual information) as a function of sample size or sample coverage (an aspect of sample completeness) is also discussed. This article is protected by copyright. All rights reserved.},
-author = {Chao, Anne and Wang, Yi-Ting and Jost, Lou},
-doi = {10.1111/2041-210x.12108},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Wang, Jost - 2013 - Entropy and the species accumulation curve a novel entropy estimator via discovery rates of new species.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {11},
-pages = {1091--1100},
-title = {{Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species}},
-url = {http://dx.doi.org/10.1111/2041-210X.12108},
-volume = {4},
-year = {2013}
-}
-@article{Halley2004,
-abstract = {Fractals have found widespread application in a range of scientific fields, including ecology. This rapid growth has produced substantial new insights, but has also spawned confusion and a host of methodological problems. In this paper, we review the value of fractal methods, in particular for applications to spatial ecology, and outline potential pitfalls. Methods for measuring fractals in nature and generating fractal patterns for use in modelling are surveyed. We stress the limitations and the strengths of fractal models. Strictly speaking, no ecological pattern can be truly fractal, but fractal methods may nonetheless provide the most efficient tool available for describing and predicting ecological patterns at multiple scales.},
-author = {Halley, J. M. and Hartley, S. and Kallimanis, A. S. and Kunin, W. E. and Lennon, J. J. and Sgardelis, S. P.},
-doi = {10.1111/j.1461-0248.2004.00568.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Halley et al. - 2004 - Uses and abuses of fractal methodology in ecology.pdf:pdf},
-journal = {Ecology Letters},
-number = {3},
-pages = {254--271},
-title = {{Uses and abuses of fractal methodology in ecology}},
-volume = {7},
-year = {2004}
-}
-@article{Bunge1993,
-abstract = {How many kinds are there? Suppose that a population is partitioned into C classes. In many situations interest focuses not on estimation of the relative sizes of the classes, but on estimation of C itself. For example, biologists and ecologists may be interested in estimating the number of species in a population of plants or animals, numismatists may be concerned with estimating the number of dies used to produce an ancient coin issue, and linguists may be interested in estimating the size of an author's vocabulary. In this article we review the problem of statistical estimation of C. Many approaches have been proposed, some purely data-analytic and others based in sampling theory. In the latter case numerous variations have been considered. The population may be finite or infinite. If finite, samples may be taken with replacement (multinomial sampling) or without replacement (hypergeometric sampling), or by Bernoulli sampling; if infinite, sampling may be multinomial or Bernoulli, or the sample may be the result of random Poisson contributions of each class. Given a sampling model, one may approach estimation of C via a parametric or nonparametric formulation; in either case there may be frequentist and Bayesian procedures. We begin by discussing the existing literature on this problem (over 120 references), organizing it by sampling model, population specification, and philosophy of estimation. We find that (a) the problem is quite resistant to statistical solution, essentially because no matter how many classes have been observed, there may still be a large number of very small unobserved classes; (b) many closely related estimation procedures have been developed independently and have not yet been compared; (c) there is not as yet a globally preferable estimator of C, although for some models there is an acceptable estimator (for some not even this is true); and (d) there are promising directions for research to pursue; for example, it appears possible to exploit estimates of the "coverage" of the sample (the total proportion of the population represented by the observed classes) to improve the accuracy of estimators of the number of classes. Finally, we make specific recommendations for future research, regarding parametric estimation, coverage-based estimation, resampling methods, Poisson process representation of sampling models, and frequentist decision theory.},
-author = {Bunge, J. and Fitzpatrick, M.},
-doi = {10.2307/2290733},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bunge, Fitzpatrick - 1993 - Estimating the number of species A review.pdf:pdf},
-journal = {Journal of the Americam Statistical Association},
-number = {421},
-pages = {364--373},
-title = {{Estimating the number of species: A review}},
-url = {https://www.jstor.org/stable/2290733},
-volume = {88},
-year = {1993}
-}
-@article{Chao2012b,
-abstract = {We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size. Traditional rarefaction or extrapolation to equal-sized samples can misrepresent the relationships between the richnesses of the communities being compared because a sample of a given size may be sufficient to fully characterize the lower diversity community, but insufficient to characterize the richer community. Thus, the traditional method systematically biases the degree of differences between community richnesses. We derived a new analytic method for seamless coverage-based rarefaction and extrapolation. We show that this method yields less biased comparisons of richness between communities, and manages this with less total sampling effort. When this approach is integrated with an adaptive coverage-based stopping rule during sampling, samples may be compared directly without rarefaction, so no extra data is taken and none is thrown away. Even if this stopping rule is not used during data collection, coverage-based rarefaction throws away less data than traditional size-based rarefaction, and more efficiently finds the correct ranking of communities according to their true richnesses. Several hypothetical and real examples demonstrate these advantages.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Chao, Anne and Jost, Lou},
-doi = {10.1890/11-1952.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Jost - 2012 - Coverage-based rarefaction and extrapolation standardizing samples by completeness rather than size.pdf:pdf},
-journal = {Ecology},
-number = {12},
-pages = {2533--2547},
-title = {{Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size}},
-url = {http://www.esajournals.org/doi/abs/10.1890/11-1952.1},
-volume = {93},
-year = {2012}
-}
-@article{Balassa1965,
-author = {Balassa, Bela},
-doi = {10.1111/j.1467-9957.1965.tb00050.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Balassa - 1965 - Trade Liberalisation and Revealed Comparative Advantage.pdf:pdf},
-journal = {The Manchester School},
-number = {2},
-pages = {99--123},
-title = {{Trade Liberalisation and "Revealed" Comparative Advantage}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9957.1965.tb00050.x/abstract},
-volume = {33},
-year = {1965}
-}
-@article{Minchin1987,
-abstract = {Simulated vegetation data were used to assess the relative robustness of ordination techniques to variations in the model of community variation in relation to environment. The methods compared were local nonmetric multidimensional scaling (LNMDS), detrended correspondence analysis (DCA), Gaussian ordination (GO), principal components analysis (PCA) and principal co-ordinates analysis (PCoA). Both LNMDS and PCoA were applied to a matrix of Bray-Curtis coefficients. The results clearly demonstrated the ineffectiveness of the linear techniques (PCA, PCoA), due to curvilinear distortion. Gaussian ordination proved very sensitive to noise and was not robust to marked departures from a symmetric, unimodal response model. The currently popular method of DCA displayed a lack of robustness to variations in the response model and the sampling pattern. Furthermore, DCA ordinations of two-dimensional models often exhibited marked distortions, even when response surfaces were unimodal and symmetric. LNMDS is recommended as a robust technique for indirect gradient analysis, which deserves more widespread use by community ecologists.},
-author = {Minchin, Peter R.},
-doi = {10.1007/BF00038690},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Minchin - 1987 - An evaluation of the relative robustness of techniques for ecological ordination.pdf:pdf},
-journal = {Vegetatio},
-number = {1-3},
-pages = {89--107},
-title = {{An evaluation of the relative robustness of techniques for ecological ordination}},
-url = {http://link.springer.com/10.1007/BF00038690},
-volume = {69},
-year = {1987}
-}
-@article{Cormack1989,
-abstract = {Log-linear models are developed for capture-recapture experiments, and their advantages and disadvantages discussed. Ways in which they can be extended, sometimes with only partial success, to open populations, subpopulations, trap dependence, and long chains of recapture periods are presented. The use of residual patterns, and analysis of subsets of data, to identify behavioural patterns and acceptable models is emphasised and illustrated with two examples.},
-annote = {Pas de support th{\'{e}}orique pour le jacknife},
-author = {Cormack, R. M.},
-doi = {10.2307/2531485},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cormack - 1989 - Log-Linear Models for Capture-Recapture.pdf:pdf},
-journal = {Biometrics},
-number = {2},
-pages = {395--413},
-title = {{Log-Linear Models for Capture-Recapture}},
-url = {http://www.jstor.org/stable/2531485},
-volume = {45},
-year = {1989}
-}
-@techreport{Nigh1997,
-abstract = {Changes in spatial distribution in regenerating lodgepole pine (Pinus contorta var. latifolia) stands were investigated during 1995-96 in British Columbia, Canada. Twenty-nine plots were established in 1993-94. Nine plots had enough ingrowth (height of {\textgreater}30 cm in 1995-96) to warrant an analysis of their spatial distribution dynamics. Ripley's K(t) statistic was used to identify the spatial pattern of trees at the initial measurement, the ingrowth trees, and the combined initial and ingrowth trees. Initial trees were mainly aggregated, but some plots had random or regularly distributed trees. Ingrowth trees were all aggregated, and initial and ingrowth trees, when analysed together, were aggregated or random. The bivariate K(t) statistic was also used to detect correlations between locations of initial and ingrowth trees. Two plots showed correlation between locations of ingrowth and initial trees. Spatial patterns were modelled by a Poisson cluster process, a Poisson process or a Markov point process when trees were aggregated, random, or regularly distributed, respectively. These models resulted in satisfactory fits. Correlation between initial and ingrowth trees occurred only when both types of trees were clustered; the correlation was modelled by using the same cluster centres to generate tree locations. When initial and ingrowth trees were uncorrelated, tree locations were generated independently.},
-author = {Nigh, G. D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nigh - 1997 - Identifying and modelling the spatial distribution dynamics of regenerating lodgepole pine.pdf:pdf},
-publisher = {Ministry of Forests, British Columbia},
-title = {{Identifying and modelling the spatial distribution dynamics of regenerating lodgepole pine}},
-url = {http://www.for.gov.bc.ca/hfd/pubs/Docs/Rr/Rr12.htm},
-year = {1997}
-}
-@article{Grau2000,
-abstract = {All individuals of Cedrela lilloi (a valuable timber species of Meliaceae) {\textgreater} 4 cm DBH were sampled in three rectangular plots (c. 15 000 m(2) each) in northwestern Argentina subtropical montane forests between 850 and 1350 m. Regeneration dynamics of C. lilloi was characterized by testing two hypotheses: (i) C. lilloi has a gap-phase regeneration mode, which implies a negative exponential size/age distribution at forest stand scale, growth releases due to canopy openings, and juvenile trees clumped at spatial scales of treefall gaps. (ii) There is a negative spatial association between adults and juveniles of C. lilloi which could be caused by density dependent mortality. Despite differences in age structure, diameter distribution approximated a negative exponential curve at all sites. Radial growth, measured as tree-ring widths, averaged between 2 and 4 mm y(-1) which is comparable to fast growing tropical species in mature forests. Aggregation of juveniles peaked at radial distances of 8 to 15 m. Size structure, growth and spatial patterns of juveniles support the first hypothesis. In support of the second hypothesis, juveniles showed a negative spatial association with conspecific mature trees at spatial scales of less than 20 m. The Janzen-Connell model of density-dependence is one potential explanation for this pattern. Although regeneration and growth patterns of C. lilloi suggest a potential for sustainable management based on small-scale gaps, spatial dynamics at stand-scale need to be considered to ensure the regeneration of mature trees.},
-annote = {Article
-English
-J TROP ECOL
-2
-308BX},
-author = {Grau, H{\'{e}}ctor Ricardo},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grau - 2000 - Regeneration patterns of Cedrela lilloi (Meliaceae) in northwestern Argentina subtropical montane forests.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {2},
-pages = {227--242},
-title = {{Regeneration patterns of Cedrela lilloi (Meliaceae) in northwestern Argentina subtropical montane forests}},
-url = {https://www.cambridge.org/core/journals/journal-of-tropical-ecology/article/regeneration-patterns-of-cedrela-lilloi-meliaceae-in-northwestern-argentina-subtropical-montane-forests/05E555D11C8A9F7D26B3C3BB14959B0B},
-volume = {16},
-year = {2000}
-}
-@article{Klier2008,
-abstract = {Using nonparametric descriptive tools developed by Duranton and Overman (2005, Review of Economic Studies, 72, 1077–1106), we show that both new and old auto supplier plants are highly concentrated in the eastern United States. Conditional logit models imply that much of this concentration can be explained parametrically by distance from Detroit, proximity to assembly plants, and access to the interstate highway system. New plants are more likely to be located in zip codes that are close to existing supplier plants. However, the degree of clustering observed is still greater than implied by the logit estimates.},
-author = {Klier, Thomas and McMillen, Daniel P},
-doi = {10.1111/j.1467-9787.2008.00549.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Klier, McMillen - 2008 - Evolving agglomeration in the U.S. auto supplier industry.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {1},
-pages = {245--267},
-title = {{Evolving agglomeration in the U.S. auto supplier industry}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9787.2008.00549.x/abstract},
-volume = {48},
-year = {2008}
-}
-@article{Podlich2002,
-abstract = {Ageneralmethodfor the analysisof ecologicalcount datawith extrazeros is presented using a Markov birth process representation of discrete distributions.The method uses a nonparametricformulationof the birth processto model the residualvariationand therefore allows the data to playa greaterrole in determiningan appropriatedistribution.This enables amore criticalassessmentof covariateeffectsandmore accuratepredictionsto bemade.The approachis also presentedas a useful diagnostictool for suggestingappropriateparametric models or verifyingstandardmodels.As an illustrativeexample,data describingabundance of a species of possum from the montane ash forests of the central highlands of Victoria, southeastAustralia, is considered. Key},
-author = {Podlich, H. M. and Faddy, M. J. and Smyth, G. K.},
-doi = {10.1198/108571102221},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podlich, Faddy, Smyth - 2002 - A general approach to modeling and analysis of species abundance data with extra zeros.pdf:pdf},
-journal = {Journal of Agricultural, Biological, and Environmental Statistics},
-number = {3},
-pages = {324--334},
-title = {{A general approach to modeling and analysis of species abundance data with extra zeros}},
-url = {http://link.springer.com/10.1198/108571102221},
-volume = {7},
-year = {2002}
-}
-@article{Amrhein1995,
-abstract = {The past few years have seen a resurging interest in the modifiable areal unit problem, or aggregation effects. The new evidence, however, both supports and conflicts with previous work. This paper represents the first stage in a series of numerical experiments designed to explore the nature and extent of scale and zonation effects. Results from a series of carefully controlled statistical simulations are reported. It is concluded that there definitely are aggregation effects separate from effects that can be attributed to changing the definition of the spatial process. These effects, however, vary with the statistic calculated. Means and variances are resistant to aggregation effects, whereas regression coefficients and correlation statistics exhibit dramatic effects. In summary, the world of spatial analysis as it relates to the modifiable areal unit problem is not entirely well-behaved, but neither is it completely random and ill-defined.},
-author = {Amrhein, C. G.},
-doi = {10.1068/a270105},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Amrhein - 1995 - Searching for the elusive aggregation effect evidence from statistical simulations.pdf:pdf},
-journal = {Environment and Planning A},
-number = {1},
-pages = {105--119},
-title = {{Searching for the elusive aggregation effect: evidence from statistical simulations}},
-url = {http://epn.sagepub.com/content/27/1/105.short},
-volume = {27},
-year = {1995}
-}
-@article{Miraldo2016,
-abstract = {The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for {\textgreater}4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27{\%} higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature.},
-author = {Miraldo, Andreia and Li, Sen and Borregaard, Michael K. and Florez-Rodriguez, A. and Gopalakrishnan, Shyam and Rizvanovic, Mirnesa and Wang, Zhiheng and Rahbek, Carsten and Marske, Katharine A. and Nogues-Bravo, D.},
-doi = {10.1126/science.aaf4381},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Miraldo et al. - 2016 - An Anthropocene map of genetic diversity.pdf:pdf},
-journal = {Science},
-number = {6307},
-pages = {1532--1535},
-title = {{An Anthropocene map of genetic diversity}},
-url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aaf4381},
-volume = {353},
-year = {2016}
-}
-@article{Mouchet2010,
-abstract = {1. Indices quantifying the functional aspect of biodiversity are essential in understanding relationships between biodiversity, ecosystem functioning and environmental constraints. Many indices of functional diversity have been published but we lack consensus about what indices quantify, how redundant they are and which ones are recommended. 2. This study aims to build a typology of functional diversity indices from artificial data sets encompassing various community structures (different assembly rules, various species richness levels) and to identify a set of independent indices able to discriminate community assembly rules. 3. Our results confirm that indices can be divided into three main categories, each of these corresponding to one aspect of functional diversity: functional richness, functional evenness and functional divergence. Most published indices are highly correlated and quantify functional richness while quadratic entropy (Q) represents a mix between functional richness and functional divergence. Conversely, two indices (FEve and FDiv respectively quantifying functional evenness and functional divergence) are rather independent to all the others. The power analysis revealed that some indices efficiently detect assembly rules while others performed poorly. 4. To accurately assess functional diversity and establish its relationships with ecosystem functioning and environmental constraints, we recommend investigating each functional component separately with the appropriate index. Guidelines are provided to help choosing appropriate indices given the issue being investigated. 5. This study demonstrates that functional diversity indices have the potential to reveal the processes that structure biological communities. Combined with complementary methods (phylogenetic and taxonomic diversity), the multifaceted framework of functional diversity will help improve our understanding of how biodiversity interacts with ecosystem processes and environmental constraints.},
-author = {Mouchet, Maud A. and Vill{\'{e}}ger, S{\'{e}}bastien and Mason, Norman W. H. and Mouillot, David},
-doi = {10.1111/j.1365-2435.2010.01695.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouchet et al. - 2010 - Functional diversity measures an overview of their redundancy and their ability to discriminate community assemb.pdf:pdf},
-journal = {Functional Ecology},
-number = {4},
-pages = {867--876},
-title = {{Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules}},
-url = {http://doi.wiley.com/10.1111/j.1365-2435.2010.01695.x},
-volume = {24},
-year = {2010}
-}
-@article{Hubert1981,
-author = {Hubert, L. J. and Golledge, R. G. and Costanzo, C. M.},
-doi = {10.1111/j.1538-4632.1981.tb00731.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hubert, Golledge, Costanzo - 1981 - Generalized procedures for evaluating spatial autocorrelation.pdf:pdf},
-journal = {Geographical Analysis},
-number = {3},
-pages = {224--233},
-title = {{Generalized procedures for evaluating spatial autocorrelation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1981.tb00731.x/abstract},
-volume = {13},
-year = {1981}
-}
-@article{Dalton1920,
-author = {Dalton, Hugh},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dalton - 1920 - The measurement of the inequality of incomes.pdf:pdf},
-journal = {The Economic Journal},
-number = {119},
-pages = {348--361},
-title = {{The measurement of the inequality of incomes}},
-volume = {30},
-year = {1920}
-}
-@article{Penttinen1992,
-abstract = {Trees in a forest interact and therefore have to be considered as a system of dependent random variates from an unknown stochastic process. One such mathematical model which considers the spatial dependence among trees in a forest and their characteristics is a marked point process. The "points" are the tree positions and the "marks" are tree characteristics such as stem diameters or tree species. Statistical methods for marked point processes can give valuable information on the spatial interaction of trees. They are applied in this paper to describe spatial dependence of stem diameters in a spruce forest, of heights of trees in a stand of pine saplings, and of heights, stem diameters, and crown lengths in a mixed birch-pine forest area.},
-author = {Penttinen, Antti and Stoyan, Dietrich and Henttonen, Helena M},
-journal = {Forest Science},
-number = {4},
-pages = {806--824},
-title = {{Marked Point Processes in Forest Statistics}},
-url = {http://www.ingentaconnect.com/content/saf/fs/1992/00000038/00000004/art00007},
-volume = {38},
-year = {1992}
-}
-@book{Davis1941,
-address = {Bloomington, Indiana},
-author = {Davis, H. T.},
-publisher = {The Principia Press},
-title = {{The theory of econometrics}},
-year = {1941}
-}
-@article{Clark1954,
-author = {Clark, Philip J. and Evans, Francis C.},
-doi = {10.2307/1931034},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clark, Evans - 1954 - Distance to nearest neighbor as a measure of spatial relationships in populations.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {445--453},
-title = {{Distance to nearest neighbor as a measure of spatial relationships in populations}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1931034/abstract},
-volume = {35},
-year = {1954}
-}
-@article{Whittaker1958,
-author = {Whittaker, R. H. and Fairbanks, C. Warren},
-doi = {10.2307/1929966},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker, Fairbanks - 1958 - A Study of Plankton Copepod Communities in the Columbia Basin , Southeastern Washington(2).pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {46--65},
-title = {{A Study of Plankton Copepod Communities in the Columbia Basin , Southeastern Washington}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1929966/full},
-volume = {39},
-year = {1958}
-}
-@article{Robinson2008,
-abstract = {We give a survey of the basic statistical ideas underlying the definition of entropy in information theory and their connections with the entropy in the theory of dynamical systems and in statistical mechanics.},
-author = {Robinson, Derek W.},
-doi = {10.3390/e10040493},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Robinson - 2008 - Entropy and uncertainty.pdf:pdf},
-journal = {Entropy},
-number = {4},
-pages = {493--506},
-title = {{Entropy and uncertainty}},
-url = {http://www.mdpi.com/1099-4300/10/4/493},
-volume = {10},
-year = {2008}
-}
-@article{Barberan2012,
-abstract = {Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing 4160000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly. The},
-author = {Barber{\'{a}}n, Albert and Bates, Scott T. and Casamayor, Emilio O. and Fierer, Noah},
-doi = {10.1038/ismej.2011.119},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barber{\'{a}}n et al. - 2012 - Using network analysis to explore co-occurrence patterns in soil microbial communities.pdf:pdf},
-journal = {The ISME Journal},
-number = {2},
-pages = {343--351},
-title = {{Using network analysis to explore co-occurrence patterns in soil microbial communities}},
-url = {http://www.nature.com/doifinder/10.1038/ismej.2011.119},
-volume = {6},
-year = {2012}
-}
-@article{Schmalensee1988,
-author = {Schmalensee, Richard},
-doi = {10.2307/2233907},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schmalensee - 1988 - Industrial Economics An Overview.pdf:pdf},
-journal = {The Economic Journal},
-number = {392},
-pages = {643--681},
-title = {{Industrial Economics: An Overview}},
-url = {https://www.jstor.org/stable/2233907},
-volume = {98},
-year = {1988}
-}
-@article{May1990a,
-author = {May, Robert M.},
-doi = {10.1038/347129a0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May - 1990 - Taxonomy as Destiny.pdf:pdf},
-journal = {Nature},
-pages = {129--130},
-title = {{Taxonomy as Destiny}},
-volume = {347},
-year = {1990}
-}
-@article{Lohbeck2012,
-abstract = {Functional diversity (FD) 'those components of biodiversity that influence how an ecosystem operates or functions' is a promising tool to assess the effect of biodiversity loss on ecosystem functioning. FD has received ample theoretical attention, but empirical studies are limited. We evaluate changes in species richness and FD during tropical secondary forest succession after shifting cultivation in Mexico. We also test whether species richness is a good predictor of FD. FD was calculated based on a combination of nine functional traits, and based on two individual traits important for primary production (specific leaf area) and carbon sequestration (wood density). Stand basal area was a good predictor of successional changes in diversity and FD, in contrast to fallow age. Incidence-based FD indices increased logarithmically with stand basal area, but FD weighted by species' importance values lacked pattern with succession. Species richness and diversity are strong predictors of FD when all traits were considered; linear relationships indicate that all species are equally functionally complementary, suggesting there is little functional redundancy. In contrast, when FD was calculated for individual traits and weighted for abundances, species richness may underestimate FD.Selection of functional trait(s) critically determines FD, with large consequences for studies relating biodiversity to ecosystem functioning. Careful consideration of the traits required to capture the ecosystem process of interest is thus essential. {\textcopyright} 2011 Perspectives in Plant Ecology, Evolution and Systematics.},
-author = {Lohbeck, Madelon and Poorter, Lourens and Paz, Horacio and Pla, Laura and van Breugel, Michiel and Mart{\'{i}}nez-Ramos, Miguel and Bongers, Frans},
-doi = {10.1016/j.ppees.2011.10.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lohbeck et al. - 2012 - Functional diversity changes during tropical forest succession.pdf:pdf},
-journal = {Perspectives in Plant Ecology, Evolution and Systematics},
-number = {2},
-pages = {89--96},
-title = {{Functional diversity changes during tropical forest succession}},
-url = {http://dx.doi.org/10.1016/j.ppees.2011.10.002},
-volume = {14},
-year = {2012}
-}
-@article{MacDonald2016,
-abstract = {Species richness and evenness, the two principle components of species diversity, are frequently used to describe variation in species assemblages in space and time. Compound indices, including variations of both the Shannon–Wiener index and Simpson's index, are assumed to intelligibly integrate species richness and evenness into all-encompassing measures. However, the efficacy of compound indices is disputed by the possibility of inverse relationships between species richness and evenness. Past studies have assessed relationships between various diversity measures across survey locations for a variety of taxa, often finding species richness and evenness to be inversely related. Butterflies are one of the most intensively monitored taxa worldwide, but have been largely neglected in such studies. Long-term butterfly monitoring programs provide a unique opportunity for analyzing how trends in species diversity relate to habitat and environmental conditions. However, analyzing trends in butterfly diversity first requires an assessment of the applicability of common diversity measures to butterfly assemblages. To accomplish this, we quantified relationships between butterfly diversity measures estimated from 10 years of butterfly population data collected in the North Saskatchewan River Valley in Edmonton, Alberta, Canada. Species richness and evenness were inversely related within the butterfly assemblage. We conclude that species evenness may be used in conjunction with richness to deepen our understandings of assemblage organization, but combining these two components within compound indices does not produce measures that consistently align with our intuitive sense of species diversity.},
-author = {MacDonald, Zachary G. and Nielsen, Scott E. and Acorn, John H.},
-doi = {10.1007/s10531-016-1261-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacDonald, Nielsen, Acorn - 2016 - Negative relationships between species richness and evenness render common diversity indices inadequa.pdf:pdf},
-journal = {Biodiversity and Conservation},
-title = {{Negative relationships between species richness and evenness render common diversity indices inadequate for assessing long-term trends in butterfly diversity}},
-url = {http://link.springer.com/10.1007/s10531-016-1261-0},
-volume = {in press},
-year = {2016}
-}
-@article{Yager1992,
-abstract = {The specificity of a possibility distribution measures the degree to which the distribution allows one and only one element as its manifestation. As such it is a measure of amount of uncertainty or information. We investigate a number of issues related to specificity measures. We discuss the connection between the specificity of a possibility distribution and the entropy of a probability distribution. We describe unifying view for constructing specificity measures. We look at the relationship of the specificity of a distribution and its negation. We consider the case where the base set is continuous.},
-author = {Yager, Ronald R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yager - 1992 - On the specificity of a possibility distribution.pdf:pdf},
-journal = {Fuzzy Sets and Systems},
-number = {3},
-pages = {279--292},
-title = {{On the specificity of a possibility distribution}},
-url = {http://www.sciencedirect.com/science/article/pii/016501149290226T},
-volume = {50},
-year = {1992}
-}
-@article{Blanc2009,
-abstract = {The expansion of selective logging in tropical forests may be an important source of global carbon emissions. However, the effects of logging practices on the carbon cycle have never been quantified over long periods of time. We followed the fate of more than 60 000 tropical trees over 23 years to assess changes in aboveground carbon stocks in 48 1.56-ha plots in French Guiana that represent a gradient of timber harvest intensities, with and without intensive timber stand improvement (TSI) treatments to stimulate timber tree growth. Conventional selective logging led to emissions equivalent to more than a third of aboveground carbon stocks in plots without TSI (85 Mg C/ha), while plots with TSI lost more than one-half of aboveground carbon stocks (142 Mg C/ha). Within 20 years of logging, plots without TSI sequestered aboveground carbon equivalent to more than 80{\%} of aboveground carbon lost to logging (-70.7 Mg C/ha), and our simulations predicted an equilibrium aboveground carbon balance within 45 years of logging. In contrast, plots with intensive TSI are predicted to require more than 100 years to sequester aboveground carbon lost to emissions. These results indicate that in some tropical forests aboveground carbon storage can be recovered within half a century after conventional logging at moderate harvest intensities.},
-annote = {Blanc, Lilian Echard, Marion Herault, Bruno Bonal, Damien Marcon, Eric Chave, Jerome Baraloto, Christopher},
-author = {Blanc, Lilian and Echard, Marion and H{\'{e}}rault, Bruno and Bonal, Damien and Marcon, Eric and Chave, J{\'{e}}r{\^{o}}me and Baraloto, Christopher},
-doi = {10.1890/08-1572.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blanc et al. - 2009 - Dynamics of aboveground carbon stocks in a selectively logged tropical forest.pdf:pdf},
-journal = {Ecological Applications},
-number = {6},
-pages = {1397--1404},
-title = {{Dynamics of aboveground carbon stocks in a selectively logged tropical forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/08-1572.1/full},
-volume = {19},
-year = {2009}
-}
-@article{Hendrickx-Candela2001,
-abstract = {Nous proposons une recension de la litt{\'{e}}rature qui {\'{e}}tudie la nature des liens entre innovation, externalit{\'{e}}s technologiques au sens d'externalit{\'{e}}s de connaissances, localisation et {\'{e}}conomies d'agglom{\'{e}}ration. Au-del{\`{a}} des liens th{\'{e}}oriques d{\'{e}}j{\`{a}} bien {\'{e}}tablis entre les deux champs disciplinaires de l'{\'{e}}conomie de l'innovation et de l'{\'{e}}conomie spatiale, ce qui nous int{\'{e}}resse particuli{\`{e}}rement, c'est de rep{\'{e}}rer les m{\'{e}}thodes et les indicateurs des analyses empiriques qui permettent de croiser ces deux champs. Nous montrons que ces deux logiques sont compl{\'{e}}mentaires et que leur croisement permet d'affiner l'explication des m{\'{e}}canismes par lesquels les {\'{e}}changes d'information et de connaissances jouent dans la formation des {\'{e}}conomies d'agglom{\'{e}}ration. Notamment, nous pouvons introduire de nouvelles variables comme les diff{\'{e}}rences sectorielles, les profils technologiques des firmes, leurs relations au sein de r{\'{e}}seaux et les caract{\'{e}}ristiques concurrentielles.},
-author = {Hendrickx-Cand{\'{e}}la, C{\'{e}}line},
-doi = {10.3917/reru.011.0011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hendrickx-Cand{\'{e}}la - 2001 - Externalit{\'{e}}s de connaissance et localisation des activit{\'{e}}s une revue des analyses empiriques.pdf:pdf},
-journal = {Revue d'Economie R{\'{e}}gionale et Urbaine},
-pages = {11--38},
-title = {{Externalit{\'{e}}s de connaissance et localisation des activit{\'{e}}s: une revue des analyses empiriques}},
-url = {https://www.cairn.info/revue-d-economie-regionale-et-urbaine-2001-1-page-11.htm},
-volume = {1},
-year = {2001}
-}
-@article{Beals1968,
-abstract = {The distribution of the shrub Cadaba rotundifolia on a sandy plain showed a complex pattern which apparently included a trend towards aggregation, and within areas of higher density a strong trend towards regularity. The latter may result from competition for water, and the former from seed dispersal. Of the various methods of analyzing departure from randomness, the ratio, observed variance to expected variance, and the index of dispersion associated with it, were the most sensitive.},
-author = {Beals, Edward W.},
-doi = {10.2307/1935538},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beals - 1968 - Spatial Pattern of Shrubs on a Desert Plain in Ethiopia.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {744--746},
-title = {{Spatial Pattern of Shrubs on a Desert Plain in Ethiopia}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1935538/full},
-volume = {49},
-year = {1968}
-}
-@article{Gower1971,
-abstract = {A general coefficient measuring the similarity between two sampling units is defined. The matrix of similarities between all pairs of sample units is shown to be positive semidefinite (except possibly when there are missing values). This is important for the multidimensional Euclidean representation of the sample and also establishes some inequalities amongst the similarities relating three individuals. The definition is extended to cope with a hierarchy of characters.},
-author = {Gower, J. C.},
-doi = {10.2307/2528823},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gower - 1971 - A General Coefficient of Similarity and Some of Its Properties.pdf:pdf},
-journal = {Biometrics},
-number = {4},
-pages = {857--871},
-title = {{A General Coefficient of Similarity and Some of Its Properties}},
-url = {http://www.jstor.org/stable/2528823},
-volume = {27},
-year = {1971}
-}
-@article{Legendre2014,
-abstract = {Aim The variation in species composition among sites, or beta diversity, can be decomposed into replacement and richness difference. A debate is ongoing in the literature concerning the best ways of computing and interpreting these indices. This paper first reviews the historical development of the formulae for decomposing dissimilarities into replacement, richness difference and nestedness indices. These formulae are presented for species presence-absence and abundance using a unified algebraic framework. The indices decomposing beta play different roles in ecological analysis than do beta-diversity indices. Innovation Replacement and richness difference indices can be interpreted and related to ecosystem processes. The pairwise index values can be summed across all pairs of sites; these sums form a valid decomposition of total beta diversity into total replacement and total richness difference components. Different communities and study areas can be compared: some may be dominated by replacement, others by richness/abundance difference processes. Within a region, differences among sites measured by these indices can then be analysed and interpreted using explanatory variables or experimental factors. The paper also shows that local contributions of replacement and richness difference to total beta diversity can be computed and mapped. A case study is presented involving fish communities along a river. Main conclusions The different forms of indices are based upon the same functional numerators. These indices are complementary; they can help researchers understand different aspects of ecosystem functioning. The methods of analysis used in this paper apply to any of the indices recently proposed. Further work, based on ecological theory and numerical simulations, is required to clarify the precise meaning and domain of application of the different forms. The forms available for presence-absence and quantitative data are both useful because these different data types allow researchers to answer different types of ecological or biogeographic questions},
-author = {Legendre, Pierre},
-doi = {10.1111/geb.12207},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre - 2014 - Interpreting the replacement and richness difference components of beta diversity.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {11},
-pages = {1324--1334},
-title = {{Interpreting the replacement and richness difference components of beta diversity}},
-url = {http://doi.wiley.com/10.1111/geb.12207},
-volume = {23},
-year = {2014}
-}
-@article{DeVienne2011,
-abstract = {Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical constraint and aim at partitioning trait values into a phylogenetic component (phylogenetic inertia) and one or multiple specific components related to adaptive evolution. The way phylogenetic information is incorporated into the PCMs depends on the method used. For the first group of methods, phylogenies are converted into variance-covariance matrices of traits following a given model of evolution such as Brownian motion (BM). For the second group of methods, phylogenies are converted into distance matrices that are subsequently transformed into Euclidean distances to perform principal coordinate analyses. Here, we show that simply taking the elementwise square root of a distance matrix extracted from a phylogenetic tree ensures having a Euclidean distance matrix. This is true for any type of distances between species (patristic or nodal) and also for trees harboring multifurcating nodes. Moreover, we illustrate that this simple transformation using the square root imposes less geometric distortion than more complex transformations classically used in the literature such as the Cailliez method. Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance-covariance matrix of a trait following a BM model, or related models of trait evolution, can be established. In that way, we build a bridge between the two groups of statistical methods widely used in comparative analysis. These results should be of great interest for ecologists and evolutionary biologists performing statistical analyses incorporating phylogenies.},
-author = {{De Vienne}, Damien M. and Aguileta, Gabriela and Ollier, S{\'{e}}bastien},
-doi = {10.1093/sysbio/syr066},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/De Vienne, Aguileta, Ollier - 2011 - Euclidean nature of phylogenetic distance matrices.pdf:pdf},
-journal = {Systematic Biology},
-number = {6},
-pages = {826--832},
-title = {{Euclidean nature of phylogenetic distance matrices}},
-url = {https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syr066},
-volume = {60},
-year = {2011}
-}
-@incollection{Nipperess2016,
-abstract = {Like other measures of diversity, Phylogenetic Diversity (PD) increases monotonically and asymptotically with increasing sample size. This relationship can be described by a rarefaction curve tracing the expected PD for a given number of accumulation units. Accumulation units represent individual organisms, collections of organisms (e.g. sites), or even species (or equivalent), giving individual-based, sample-based and species-based curves respectively. The formulation for the exact analytical solution for the rarefaction of PD is given in an expanded form to demonstrate congruence with the classic formulation for the rarefaction of species richness. Rarefaction is commonly applied as a standardisation for diversity values derived from differing numbers of sampling units. However, the solution can be simply extended to create measures of phylogenetic evenness, phylogenetic beta-diversity and phylogenetic dispersion, derived from individual-based, sample-based and species-based curves respectively. This extension, termed ∆PD, is simply the initial slope of the rarefaction curve and is related to entropy measures such as PIE (Probability of Interspecific Encounter) and Gini-Simpson entropy. The application of rarefaction of PD to sample standardisation and measurement of phylogenetic evenness, phylogenetic beta-diversity and phylogenetic dispersion is demonstrated. Future prospects for PD rarefaction include the recognition of evolutionary hotspots (independent of species richness), the basis for ecological theory such as phylogeny-area relationships, and the prediction of unseen biodiversity.},
-author = {Nipperess, David A.},
-booktitle = {Biodiversity Conservation and Phylogenetic Systematics},
-doi = {10.1007/978-3-319-22461-9},
-editor = {Pellens, Roseli and Grandcolas, Philippe},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nipperess - 2016 - The Rarefaction of Phylogenetic Diversity Formulation, Extension and Application.pdf:pdf},
-isbn = {978-3-319-22460-2},
-pages = {197--217},
-publisher = {Springer Open},
-title = {{The Rarefaction of Phylogenetic Diversity: Formulation, Extension and Application}},
-url = {http://link.springer.com/10.1007/978-3-319-22461-9},
-year = {2016}
-}
-@article{Castellani2016,
-abstract = {Probability distributions have proven effective at modeling diversity in complex systems. The two most common are the Gaussian normal and skewed-right. While the mechanics of the former are well-known; the latter less so, given the significant limitations of the power-law. Moving past the power-law, we demonstrate that there exists, hidden-in-full-view, a limiting law governing the diversity of complexity in skewed-right systems; which can be measured using a case-based version math formula of Shannon entropy, resulting in a 60/40 rule. For our study, given the wide range of approaches to measuring complexity (i.e., descriptive, constructive, etc), we examined eight different systems, which varied significantly in scale and composition (from galaxies to genes). We found that skewed-right complex systems obey the law of restricted diversity; that is, when plotted for a variety of natural and human-made systems, as the diversity of complexity math formula (primarily in terms of the number of types; but also, secondarily, in terms of the frequency of cases) a limiting law of restricted diversity emerges, constraining the majority of cases to simpler types. Even more compelling, this limiting law obeys a scale-free 60/40 rule: when measured using math formula, 60{\%}(or more) of the cases in these systems reside within the first 40{\%} (or less) of the lower bound of equiprobable diversity types—with or without long-tail and whether or not the distribution fits a power-law. Furthermore, as an extension of the Pareto Principle, this lower bound accounts for only a small percentage of the total diversity; that is, while the top 20{\%} of cases constitute a sizable percentage of the total diversity in a system, the bottom 60{\%} are highly constrained. In short, as the central limit theorem governs the diversity of complexity in normal distributions, restricted diversity seems to govern the diversity of complexity in skewed-right distributions.},
-author = {Castellani, Brian and Rajaram, Rajeev},
-doi = {10.1002/cplx.21786},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Castellani, Rajaram - 2016 - Past the power law Complex systems and the limiting law of restricted diversity.pdf:pdf},
-journal = {Complexity},
-month = {nov},
-number = {S2},
-pages = {99--112},
-title = {{Past the power law: Complex systems and the limiting law of restricted diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/cplx.21786/abstract},
-volume = {21},
-year = {2016}
-}
-@article{Mortier2015,
-abstract = {Understanding how environmental factors could impact population dynamics is of primary importance for species conservation. Matrix population models are widely used to predict population dynamics. However, in species-rich ecosystems with many rare species, the small population sizes hinder a good fit of species-specific models. In addition, classical matrix models do not take into account environmental variability. We propose a mixture of regression models with variable selection allowing the simultaneous clustering of species into groups according to vital rate information (recruitment, growth and mortality) and the identification of group-specific explicative environmental variables. We develop an inference method coupling the R packages flexmix and glmnet. We first highlight the effectiveness of the method on simulated datasets. Next, we apply it to data from a tropical rain forest in the Central African Republic. We demonstrate the accuracy of the inhomogeneous mixture matrix model in successfully reproducing stand dynamics and classifying tree species into well-differentiated groups with clear ecological interpretations.},
-author = {Mortier, Fr{\'{e}}d{\'{e}}ric and Ou{\'{e}}draogo, Dakis-Yaoba and Claeys, Florian and Tadesse, Mahlet G. and Cornu, Guillaume and Baya, Fid{\`{e}}le and Benedet, Fabrice and Freycon, Vincent and Gourlet-Fleury, Sylvie and Picard, Nicolas},
-doi = {10.1002/env.2320},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mortier et al. - 2015 - Mixture of inhomogeneous matrix models for species-rich ecosystems.pdf:pdf},
-journal = {Environmetrics},
-number = {1},
-pages = {39--51},
-title = {{Mixture of inhomogeneous matrix models for species-rich ecosystems}},
-url = {http://doi.wiley.com/10.1002/env.2320},
-volume = {26},
-year = {2015}
-}
-@article{Baraloto2010a,
-abstract = {P{\textgreater}Cross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy towards a whole-plant approach by integrating data on functional traits for 13 448 leaves and wood tissues from 4672 trees representing 668 species of Neotropical trees. Strong correlations amongst traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover vs. costly physical leaf structure with a long revenue stream. A second axis of variation, the 'stem economics spectrum', defines a similar tradeoff at the stem level: dense wood vs. high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.},
-author = {Baraloto, Christopher and Paine, C. E. Timothy and Poorter, Lourens and Beauch{\^{e}}ne, Jacques and Bonal, Damien and Domenach, Anne-Marie and H{\'{e}}rault, Bruno and Pati{\~{n}}o, Sandra and Roggy, Jean-Christophe and Chave, J{\'{e}}r{\^{o}}me},
-doi = {10.1111/j.1461-0248.2010.01517.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2010 - Decoupled leaf and stem economics in rain forest trees.pdf:pdf},
-journal = {Ecology Letters},
-number = {11},
-pages = {1338--1347},
-title = {{Decoupled leaf and stem economics in rain forest trees}},
-volume = {13},
-year = {2010}
-}
-@article{Cavender-Bares2006,
-abstract = {Consideration of the scale at which communities are defined both taxonomically and spatially can reconcile apparently contradictory results on the extent to which plants show phylogenetic niche conservatism. In plant communities in north central Florida, we collected species abundances in 55 0.1-ha plots in several state parks. When communities were defined narrowly to include a single phylogenetic lineage, such as Quercus, Pinus, or Ilex, neighbors tended to be less related than expected (phylogenetic overdispersion) or there was no pattern. If the same communities were defined more broadly, such as when all seed plants were included, neighbors tended to be more related than expected (phylogenetic clustering). These results provide evidence that species interactions among close relatives influence community structure, but they also show that niche conservatism is increasingly evident as communities are defined to include greater phylogenetic diversity. We also found that, as the spatial scale is increased to encompass greater environmental heterogeneity, niche conservatism emerges as the dominant pattern. We then examined patterns of trait evolution in relation to trait similarity within communities for 11 functional traits for a single phylogenetic lineage (Quercus) and for all woody plants. Among the oaks, convergent evolution of traits important for environmental filtering contributes to the observed pattern of phylogenetic overdispersion. At the broader taxonomic scale, traits tend to be conserved, giving rise to phylogenetic clustering. The shift from overdispersion to clustering can be explained by the increasing conservatism of traits at broader phylogenetic scales. {\^{A}}{\textcopyright} 2006 by the Ecological Society of America.},
-annote = {Cited By (since 1996): 91
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: ECOLA
-PubMed ID: 16922307
-Language of Original Document: English
-Correspondence Address: Cavender-Bares, J.; Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, United States; email: cavender@umn.edu},
-author = {Cavender-Bares, Jeannine and Keen, Adrienne and Miles, Brianna},
-doi = {10.1890/0012-9658(2006)87[109:PSOFPC]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cavender-Bares, Keen, Miles - 2006 - Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale.pdf:pdf},
-journal = {Ecology},
-number = {7 Supplement},
-pages = {S109--S122},
-title = {{Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282006{\%}2987[109:PSOFPC]2.0.CO;2/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Lazarina2013,
-abstract = {* Beta diversity provides a link between species diversity in a region to species diversity within sites. Many metrics have been proposed for its estimation each reflecting a different aspect of the phenomenon. Many of them are more informative of the variation in alpha diversity among samples and the sampling effort (number of sampling units) rather than of the species assemblage differentiation. Here, we propose an index based on the sampling effort needed to fulfil a certain criterion and accounts for the relationship between the initial slope of the species accumulation curve and mean alpha diversity. * For defining the index, we consider a set of n samples with S(n) species among R(n) total occurrences. The shared species occurrences are I(n) = R(n) − S(n). The proposed new index (N*) is defined as the point, in terms of n, where I(n) crosses S(n). Samples taken beyond that point (N*) contribute, cumulatively, more to the shared occurrences rather than to new species. For the estimation of N*, we provide the R function ‘Nstar' based on the specaccum function in the vegan package. * We tested the properties of N* on simulated datasets with known community assembly patterns and on a dataset of plant diversity of Greek Natura 2000 protected areas. * N* is not mathematically confounded with alpha or gamma diversity. It depends on the relationship between gamma and alpha (Whittaker's index) but, furthermore, it reflects the variation in species occupancies. Thus, if a number of random samples, sufficient for the reliable estimation of mean alpha diversity and the species accumulation curve, is collected, N* converges to a value that does not change by the inclusion of more samples from the same region. N* depends primarily on the proportion of new species expected in each next sample. * N* declines with nestedness in community structure, while it increases with species turnover. This holds for plant diversity of Greek Natura 2000, where N* exhibited lower values in island compared to continental regions reflecting the increased nestedness of island communities.},
-author = {Lazarina, Maria and Sgardeli, Vasiliki and Kallimanis, Athanasios S and Sgardelis, Stefanos P},
-doi = {10.1111/2041-210x.12013},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lazarina et al. - 2013 - An effort-based index of beta diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {217--225},
-title = {{An effort-based index of beta diversity}},
-url = {http://dx.doi.org/10.1111/2041-210x.12013},
-volume = {4},
-year = {2013}
-}
-@incollection{Leigh2004,
-address = {Chicago and London},
-author = {Leigh, E. G. Jr.},
-booktitle = {Tropical forest diversity and dynamism - Findings from a Large-Scale plot network},
-edition = {The Univer},
-editor = {Losos, Elizabeth and Leigh, Egbert},
-pages = {315--317},
-title = {{Part 6 : The diversity of tropical trees : the role of pest pressure}},
-year = {2004}
-}
-@article{Borruso2008,
-abstract = {Human activities and more generally the phenomena related to human behaviour take place in a network-constrained subset of the geographical space. These phenomena can be expressed as locations having their positions configured by a road network, as address points with street numbers. Although these events are considered as points on a network, point pattern analysis and the techniques implemented in a GIS environment generally consider events as taking place in a uniform space, with distance expressed as Euclidean and over a homogeneous and isotropic space. Network-spatial analysis has developed as a research agenda where the attention is drawn towards point pattern analytical techniques applied to a space constrained by a road network. Little attention has been put on first order properties of a point pattern (i.e. density) in a network space, while mainly second order analysis such as nearest neighbour and K-functions have been implemented for network configurations of the geographical space. In this article, a method for examining clusters of human-related events on a network, called Network Density Estimation (NDE), is implemented using spatial statistical tools and GIS packages. The method is presented and compared to conventional first order spatial analytical techniques such as Kernel Density Estimation (KDE). Network Density Estimation is tested using the locations of a sample of central, urban activities associated with bank and insurance company branches in the central areas of two midsize European cities, Trieste (Italy) and Swindon (UK). [ABSTRACT FROM AUTHOR] Copyright of Transactions in GIS is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.},
-author = {Borruso, Giuseppe},
-doi = {10.1111/j.1467-9671.2008.01107.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borruso - 2008 - Network density estimation A GIS approach for analysing point patterns in a network space.pdf:pdf},
-journal = {Transactions in GIS},
-number = {3},
-pages = {377--402},
-title = {{Network density estimation: A GIS approach for analysing point patterns in a network space}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9671.2008.01107.x/abstract},
-volume = {12},
-year = {2008}
-}
-@article{Acar1999,
-abstract = {This research note investigates the trend towards specializing the Herfindahl index H for measuring industry concentration and the entropy measure E for expressing firm diversity. Examining the " decomposability " of E and H, we show that the professed overriding advantage of the entropy measure with respect to decomposability is not its exclusive preserve; the paper contains a proof that this property is also shared by the Herfindahl index. It is also shown that, due to its more stable range, the H index is more versatile with respect to inversion than the E measure. Strategy researchers are thereby cautioned that the current trend toward an increased use of entropy is risky and should be reassessed.},
-author = {Acar, William and Sankaran, Kizhekepat},
-doi = {10.1002/(SICI)1097-0266(199910)20:10<969::AID-SMJ57>3.0.CO;2-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Acar, Sankaran - 1999 - The myth of the unique decomposability specializing the Herfindahl and entropy measures.pdf:pdf},
-journal = {Strategic Management Journal},
-number = {10},
-pages = {969--975},
-title = {{The myth of the unique decomposability: specializing the Herfindahl and entropy measures?}},
-url = {http://doi.wiley.com/10.1002/{\%}28SICI{\%}291097-0266{\%}28199910{\%}2920{\%}3A10{\%}3C969{\%}3A{\%}3AAID-SMJ57{\%}3E3.0.CO{\%}3B2-0},
-volume = {20},
-year = {1999}
-}
-@article{Jost2008,
-abstract = {G(ST) and its relatives are often interpreted as measures of differentiation between subpopulations, with values near zero supposedly indicating low differentiation. However, G(ST) necessarily approaches zero when gene diversity is high, even if subpopulations are completely differentiated, and it is not monotonic with increasing differentiation. Likewise, when diversity is equated with heterozygosity, standard similarity measures formed by taking the ratio of mean within-subpopulation diversity to total diversity necessarily approach unity when diversity is high, even if the subpopulations are completely dissimilar (no shared alleles). None of these measures can be interpreted as measures of differentiation or similarity. The derivations of these measures contain two subtle misconceptions which cause their paradoxical behaviours. Conclusions about population differentiation, gene flow, relatedness, and conservation priority will often be wrong when based on these fixation indices or similarity measures. These are not statistical issues; the problems persist even when true population frequencies are used in the calculations. Recent advances in the mathematics of diversity identify the misconceptions, and yield mathematically consistent descriptive measures of population structure which eliminate the paradoxes produced by standard measures. These measures can be directly related to the migration and mutation rates of the finite-island model.},
-annote = {Times Cited: 72},
-author = {Jost, Lou},
-doi = {10.1111/j.1365-294X.2008.03887.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2008 - GST and its relatives do not measure differentiation.pdf:pdf},
-journal = {Molecular Ecology},
-number = {18},
-pages = {4015--4026},
-title = {{GST and its relatives do not measure differentiation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2008.03887.x/abstract},
-volume = {17},
-year = {2008}
-}
-@article{Webb2002,
-abstract = {As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.},
-annote = {Cited By (since 1996): 463
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: ARECB
-doi: 10.1146/annurev.ecolsys.33.010802.150448
-Language of Original Document: English
-Correspondence Address: Webb, C.O.; Department of Ecology, Yale University, New Haven, CT 06511, United States; email: campbell.webb@yale.edu},
-author = {Webb, Campbell O. and Ackerly, David D. and McPeek, Mark A. and Donoghue, Michael J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Webb et al. - 2002 - Phylogenies and community ecology.pdf:pdf},
-journal = {Annual Review of Ecology and Systematics},
-pages = {475--505},
-title = {{Phylogenies and community ecology}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0036909621{\&}partnerID=40{\&}md5=0fb723d1cad92ca86d251fa01182984a},
-volume = {33},
-year = {2002}
-}
-@article{Herault2007,
-abstract = {Question: To establish a habitat classification based on functional group co-occurrence that may help the drawing up of conservation plans. Location: Riverine forest fragments in the Grand-duch{\'{e}} de Luxembourg, Europe. Methods: Forest fragments were surveyed for their abundance of vascular plants. These were clustered into emergent groups according to 14 life-traits related to plant dispersal, establishment and persistence. Forest fragments were classified according to similar distribution of the identified emergent groups. Environmental factors were related to the emergent group richness in each forest type using generalized linear models. Results: Contrary to former species centred classifications, only two groups of forests, each with clearly different emergent group composition and conservation requirements, were detected: (1) swamp forests characterized by anemogamous perennials, annuals and hydrochorous perennials and (2) moist forests characterized by barochorous perennials, small geophytes and zoochorous phanerophytes. From a conservation point of view, priority should be given to large swamp forest with intact flooding regimes. This is in accordance with the high wind and water dispersal capacities of their typical emergent groups. For the moist forests, conservation priorities should be high forest connectivity and historical continuity since dispersal and establishment of their characteristic emergent groups are highly limited. Conclusions: The described methodology, situated at an intermediate integration level between the individual species and whole community descriptors, takes advantage of both conservation plans built for single species and the synthetic power of broad ecological measures.},
-author = {H{\'{e}}rault, Bruno and Honnay, O.},
-doi = {10.1658/1402-2001(2007)10[73:Ulttaa]2.0.Co;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/H{\'{e}}rault, Honnay - 2007 - Using life-history traits to achieve a functional classification of habitats.pdf:pdf},
-journal = {Applied Vegetation Science},
-number = {1},
-pages = {73--80},
-title = {{Using life-history traits to achieve a functional classification of habitats}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-109X.2007.tb00505.x/abstract},
-volume = {10},
-year = {2007}
-}
-@article{Frohlich1995,
-abstract = {This paper describes the analysis of spatial patterns formed by natural regeneration in mixed mountain forest stands. The coordinates of the plants were taken in circular quadrats which were regularly arranged in plots distributed within the research areas. We analysed first univariate patterns, both for all regenerations pooled together and for the main tree species separately, and second bivariate patterns for all combinations of main tree species. The patterns were described by indices measuring the deviation from randomness at different scales-from nearest-neighbor to whole-quadrat level. For each index we performed a three-step test procedure which gave a multiple error probability for the null hypothesis of overall randomness. The analyses showed no pronounced deviation from a random distribution within quadrats of 1 m, although the univariate patterns tend to a very slight aggregation. At larger scales we observe significant univariate aggregation and bivariate segregation. Bivariate association may also be present, but could not be confirmed.},
-author = {Fr{\"{o}}hlich, M. and Quednau, H. D.},
-doi = {10.1016/0378-1127(94)03504-P},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fr{\"{o}}hlich, Quednau - 1995 - Statistical analysis of the distribution pattern of natural regeneration in forests.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {45--57},
-title = {{Statistical analysis of the distribution pattern of natural regeneration in forests}},
-url = {http://www.sciencedirect.com/science/article/pii/037811279403504P},
-volume = {73},
-year = {1995}
-}
-@article{Stoffels2003,
-abstract = {Understanding the constraints on community composition at multiple spatial scales is an immense challenge to community and ecosystem ecologists. As community composition is basically the composite result of species' spatial patterning, studying this spatial patterning across scales may yield clues as to which scales of environmental heterogeneity influence communities. The now widely documented positive interspecific relationship between 'regional' range and mean 'local' abundance has become a generalisation describing the spatial patterning of species at coarse scales. We address some of the shortcomings of this generalisation, as well as examine the cross-scale spatial patterning (aggregation and density levels) of littoral-benthic invertebrates in very large lakes. Specifically, we (a) determine whether the positive range-abundance relationship can be reinterpreted in terms of the actual spatial structure of species distributions, (b) examine the relationship between aggregation and density across different spatial scales, and (c) determine whether the spatial patterning of species (e.g. low density/aggregated distribution) is constant across scales, that is, whether our interpretation of a species spatial pattern is dependent on the scale at which we choose to observe the system.Spatial aggregation of littoral invertebrates was generally a negative function of mean density across all spatial scales and seasons (autumn and spring). This relationship may underlie positive range-abundance relationships. Species that were uncommon and highly aggregated at coarse spatial scales can be abundant and approach random distributions at finer spatial scales. Also, the change in spatial aggregation of closely related taxa across spatial scales was idiosyncratic. The idiosyncratic cross-scale spatial patterning of species implies that multiple scales of environmental heterogeneity may influence the assembly of littoral communities. Due to the multi-scale, species-specific spatial patterning of invertebrates, littoral zone communities form a complex spatial mosaic, and a 'spatially explicit' approach will be required by limnologists in order to link littoral-benthic community patterns with ecosystem processes in large oligotrophic lakes.},
-author = {Stoffels, Rick J. and Closs, Gerard P. and Burns, Carolyn W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoffels, Closs, Burns - 2003 - Multiple scales and the relationship between density and spatial aggregation in littoral zone communitie.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {81--92},
-title = {{Multiple scales and the relationship between density and spatial aggregation in littoral zone communities}},
-volume = {103},
-year = {2003}
-}
-@article{Spooner2004,
-abstract = {Spatial patterning of plant distributions has long been recognised as being important in understanding underlying ecological processes. Ripley's K-function is a frequently used method for studying the spatial pattern of mapped point data in ecology. However, application of this method to point patterns on road networks is inappropriate, as the K-function assumes an infinite homogenous environment in calculating Euclidean distances. A new technique for analysing the distribution of points on a network has been developed, called the network K-function (for univariate analysis) and network cross K-function (for bivariate analysis). To investigate its applicability for ecological data-sets, this method was applied to point location data for roadside populations of three Acacia species in a fragmented agricultural landscape of south-eastern Australia. Kernel estimations of the observed density of spatial point patterns for each species showed strong spatial heterogeneity. Combined univariate and bivariate network K-function analyses confirmed significant clustering of populations at various scales, and spatial patterns of Acacia decora suggests that roadworks activities may have a stronger controlling influence than environmental determinants on population dynamics. The network K-function method will become a useful statistical tool for the analyses of ecological data along roads, field margins, streams and other networks.},
-author = {Spooner, Peter G. and Lunt, Ian D. and Okabe, Atsuyuki and Shiode, Shino},
-doi = {10.1023/B:LAND.0000036114.32418.d4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Spooner et al. - 2004 - Spatial analysis of roadside Acacia populations on a road network using the network K-function.pdf:pdf},
-journal = {Landscape Ecology},
-number = {5},
-pages = {491--499},
-title = {{Spatial analysis of roadside Acacia populations on a road network using the network K-function}},
-url = {http://link.springer.com/article/10.1023/B:LAND.0000036114.32418.d4},
-volume = {19},
-year = {2004}
-}
-@article{Chiu2014b,
-abstract = {Hill numbers (or the "effective number of species") are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify "the effective number of equally abundant and (functionally) equally distinct species" in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, S{\o}rensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.},
-author = {Chiu, Chun-Huo and Chao, Anne},
-doi = {10.1371/journal.pone.0100014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu, Chao - 2014 - Distance-based functional diversity measures and their decomposition a framework based on hill numbers.pdf:pdf},
-journal = {PloS one},
-number = {7},
-pages = {e100014},
-title = {{Distance-based functional diversity measures and their decomposition: a framework based on hill numbers}},
-url = {http://www.plosone.org/article/info{\%}253Adoi{\%}252F10.1371{\%}252Fjournal.pone.0100014},
-volume = {9},
-year = {2014}
-}
-@article{Hankin2007,
-abstract = {The distribution of abundance amongst species with similar ways of life is a classical problem in ecology. The unified neutral theory of biodiversity, due to Hubbell, states that observed population dynamics may be explained on the assumption of per capita equivalence amongst individuals. One can thus dispense with differences between species, and differences between abundant and rare species: all individuals behave alike in respect of their probabilities of reproducing and death. It is a striking fact that such a parsimonious theory results in a non-trivial dominancediversity curve (that is, the simultaneous existence of both abundant and rare species) and even more striking that the theory predicts abundance curves that match observations across a wide range of ecologies. This paper introduces the untb package of R routines, for numerical simulation of ecological drift under the unified neutral theory. A range of visualization, analytical, and simulation tools are provided in the package and these are presented with examples in the paper.},
-author = {Hankin, Robin K. S.},
-doi = {10.18637/jss.v022.i12},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hankin - 2007 - Introducing untb, an R Package For Simulating Ecological Drift Under the Unified Neutral Theory of Biodiversity.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {12},
-pages = {1--15},
-title = {{Introducing untb, an R Package For Simulating Ecological Drift Under the Unified Neutral Theory of Biodiversity}},
-url = {http://www.jstatsoft.org/v22/i12/paper},
-volume = {22},
-year = {2007}
-}
-@article{Loreau2000,
-abstract = {A popular way to suggest a regional influence on local species diversity has been to plot local versus regional diversity. The form of these curves has been interpreted as evidence for or against "community saturation" due to species interactions. This interpretation, however, is unwarranted. Using the concepts of alpha, beta and gamma diversity, I show that local-regional richness curves are determined by the way total diversity is partitioned between its alpha and beta components, which itself is a matter of scale. Changing the scale of the local community amounts to changing the scale at which the heterogeneity of the interactions between organisms and their environment manifests itself, and hence the balance between alpha and beta diversity. Community saturation may occur because of physical limitations, but there are no theoretical grounds for the belief that species interactions set an absolute upper limit to diversity at any scale. A distinction between different meanings of the concept of "saturation" is proposed to clarify this issue. I argue that the challenge now is to understand the relationship between alpha and beta diversity at multiple scales, and the processes that determine it.},
-annote = {ISI Document Delivery No.: 296JK
-Times Cited: 193
-Cited Reference Count: 20
-BLACKWELL SCIENCE LTD},
-author = {Loreau, Michel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau - 2000 - Are communities saturated On the relationship between alpha, beta and gamma diversity.pdf:pdf},
-journal = {Ecology Letters},
-number = {2},
-pages = {73--76},
-title = {{Are communities saturated? On the relationship between alpha, beta and gamma diversity}},
-volume = {3},
-year = {2000}
-}
-@article{Scotti2015,
-abstract = {Key message Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical tree V. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree's contribution to regeneration. Results Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii.},
-author = {Scotti, Ivan and Montaigne, William and Cseke, Kl{\'{a}}ra and Traissac, St{\'{e}}phane},
-doi = {10.1007/s13595-015-0508-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scotti et al. - 2015 - Life after disturbance (II) the intermediate disturbance hypothesis explains genetic variation in forest gaps dom.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {8},
-pages = {1035--1042},
-title = {{Life after disturbance (II): the intermediate disturbance hypothesis explains genetic variation in forest gaps dominated by Virola michelii Heckel (Myristicaceae)}},
-url = {http://link.springer.com/10.1007/s13595-015-0508-3},
-volume = {72},
-year = {2015}
-}
-@article{Egler1954,
-abstract = {Two principles are considered as being involved in vegetation development on abandoned agricultural lands. The first, called Relay Floristics, involves a succession of incoming and outgoing plants, each group invading the land, ousting its predecessor, and in turn preparing the site so as to be ousted itself. This is the conventional interpretation of “old-field plant succession”, but is considered by the author to be in many cases a very minor principle. The second principle is called Initial Floristic Composition, and refers to that element which invades or has invaded at the time of abandonment. Following abandonment, there is a progressive development, with the forbs and grasses assuming predominance first, and the trees last. An evaluation of the relative importance of these two principles is necessary in Vegetation Management. For example, with Init. Flor. Comp. primary, the selective elimination of some elements of the flora can produce new and often stable plant communities. Thereafter such communities change only by the very different and often slowly acting principle of Relay Floristics. Relay Floristics itself can be modified and controlled by encouraging those plant covers which are most or least resistant to invasion to incoming relays of significance to the management plant.},
-author = {Egler, Frank E.},
-doi = {10.1007/BF00275587},
-isbn = {0042-3106},
-issn = {00423106},
-journal = {Vegetatio Acta Geobotanica},
-number = {6},
-pages = {412--417},
-pmid = {240},
-title = {{Vegetation science concepts I. Initial floristic composition, a factor in old-field vegetation development with 2 figs.}},
-volume = {4},
-year = {1954}
-}
-@article{Berman1989,
-abstract = {This paper considers the nonparametric estimation of the integral J = S( tL(t)p(t)dt where L(t) is the unknown second-order intensity function of a two-dimensional stationary isotropic point process observed in some region and p( t) is known for t E [O, T]. An unbiased estimator of J is derived, and a computationally fast approximation to it is proposed. The estimator is then used to obtain a kernel method for smoothing point process data, a new estimator of the Fourier transform of the second-order intensity and some tests for spatial association between a point process and another stochastic process.},
-author = {Berman, Mark and Diggle, Peter J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Berman, Diggle - 1989 - Estimating Weighted Integrals of the Second-Order Intensity of a Spatial Point Process.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {81--92},
-title = {{Estimating Weighted Integrals of the Second-Order Intensity of a Spatial Point Process}},
-volume = {51},
-year = {1989}
-}
-@article{Leininger2014,
-abstract = {Spatial point pattern data describes locations of events observed over a given domain, with the number of and locations of these events being random. Historically, data analysis for spatial point patterns has focused on rejecting complete spatial randomness and then on fitting a richer model specification. From a Bayesian standpoint, the literature is growing but primarily considers versions of Poisson processes, focusing on specifications for the intensity. However, the Bayesian literature on, e.g., clustering or inhibition processes is limited, primarily attending to model fitting. There is little attention given to full inference and scant with regard to model adequacy or model comparison. The contribution here is full Bayesian analysis, implemented through generation of posterior point patterns using composition. Model features, hence broad inference, can be explored through functions of these samples. The approach is general, applicable to any generative model for spatial point patterns. The approach is also useful in considering model criticism and model selection both in-sample and, when possible, out-of-sample. Here, we adapt or extend familiar tools. In particular, for model criticism, we consider Bayesian residuals, realized and predictive, along with empirical coverage and prior predictive checks through Monte Carlo tests. For model choice, we propose strategies using predictive mean square error, empirical coverage, and ranked probability scores. For simplicity, we illustrate these methods with standard models such as Poisson processes, log-Gaussian Cox processes, and Gibbs processes. The utility of our approach is demonstrated using a simulation study and two real datasets.},
-author = {Leininger, Thomas J. and Gelfand, Alan E.},
-doi = {10.1214/15-BA985},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leininger, Gelfand - 2015 - Bayesian Inference for Spatial Point Patterns.pdf:pdf},
-journal = {Bayesian Analysis},
-number = {1},
-pages = {1--30},
-title = {{Bayesian Inference and Model Assessment for Spatial Point Patterns Using Posterior Predictive Samples}},
-url = {http://projecteuclid.org/euclid.ba/1448899901},
-volume = {12},
-year = {2015}
-}
-@misc{Chao2016c,
-author = {Chao, Anne and Ma, K. H. and Hsieh, T. C. and Chiu, Chun-Huo},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2016 - SpadeR Species Prediction and Diversity Estimation with R.pdf:pdf},
-title = {{SpadeR: Species Prediction and Diversity Estimation with R}},
-url = {http://chao.stat.nthu.edu.tw/blog/software-download/},
-year = {2016}
-}
-@article{Rosindell2010,
-abstract = {In response to a seemingly unresolvable plethora of explanations of how, especially in tropical settings, so many kinds of trees can coexist, Hubbell (1997, 2001) proposed neutral theory to explain biodiversity patterns without invoking species differences. Neutral theory assumes that each individual's prospects of death and reproduction are independent of what species it, or its neighbors, belong to (Hubbell 2001). This assumption is simple enough to allow neutral theory to unify diverse aspects of ecology and biogeography such as species abundance distributions, changes in species composition over space and time, and the impacts of habitat fragmentation in a “unified neutral theory of biodiversity and biogeography” (Hubbell, 2001). Hubbell's theory is modeled on neutral theory in population genetics, where within a species, each individual's prospects of death and reproduction are independent of its genotype (Kimura, 1983). Ecologists apply neutral theory within a single trophic level, usually trees, sometimes corals or other guilds (Hubbell, 1997, 2001).},
-author = {Leigh, Egbert G. Jr and Rosindell, James and Etienne, Rampal S.},
-doi = {10.4249/scholarpedia.8822},
-journal = {Scholarpedia},
-pages = {8822},
-title = {{Unified neutral theory of biodiversity and biogeography}},
-url = {http://www.scholarpedia.org/article/Unified{\_}neutral{\_}theory{\_}of{\_}biodiversity{\_}and{\_}biogeography},
-volume = {5},
-year = {2010}
-}
-@article{Veron2015,
-abstract = {The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.},
-author = {Veron, Simon and Davies, T. Jonathan and Cadotte, Marc W. and Clergeau, Philippe and Pavoine, Sandrine},
-doi = {10.1111/brv.12228},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veron et al. - 2015 - Predicting loss of evolutionary history Where are we.pdf:pdf},
-journal = {Biological Reviews},
-number = {1},
-pages = {271--291},
-title = {{Predicting loss of evolutionary history: Where are we?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/brv.12228/abstract},
-volume = {92},
-year = {2017}
-}
-@article{Skellam1952,
-author = {Skellam, J. G.},
-doi = {10.2307/2334030},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Skellam - 1952 - Studies in statistical ecology. I, Spatial pattern.pdf:pdf},
-journal = {Biometrika},
-number = {3/4},
-pages = {346--362},
-title = {{Studies in statistical ecology. I, Spatial pattern.}},
-url = {http://www.jstor.org/stable/2334030},
-volume = {39},
-year = {1952}
-}
-@article{Wills1999,
-abstract = {Quadrat-based analysis of two rainforest plots of area 50 ha, one in Panama (Barro Colorado Island, BCI) and the other in Malaysia (Pasoh), shows that in both plots recruitment is in general negatively correlated with both numbers and biomass of adult trees of the same species in the same quadrat. At BCI, this effect is not significantly influenced by treefall gaps. In both plots, recruitment of individual species is negatively correlated with the numbers of trees of all species in the quadrats, but not with overall biomass. These observations suggest, but do not prove, widespread frequency-dependent effects produced by pathogens and seed-predators that act most effectively in quadrats crowded with trees. Within-species correlations of mortality with numbers or biomass are not found in either plot, indicating that most frequency-dependent mortality takes place before the trees reach cm in diameter. Stochastic effects caused by BCI's more rapid tree turnover may contribute to a larger variance in diversity from quadrat to quadrat at BCI, although they are not sufficient to explain why BCI has fewer than half as many tree species as Pasoh. Finally, in both plots quadrats with low diversity show a significant increase in diversity over time, and this increase is stronger at BCI. This process, like the frequency-dependence, will tend to maintain diversity over time. In general, these non-random forces that should lead to the maintenance of diversity are slightly stronger at BCI, even though the BCI plot is less diverse than the Pasoh plot. Keywords:},
-author = {Wills, Christopher and Condit, Richard},
-doi = {10.1098/rspb.1999.0799},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wills, Condit - 1999 - Similar Non-Random Processes Maintain Diversity in Two Tropical Rainforests.pdf:pdf},
-journal = {Proceedings: Biological Sciences},
-number = {1427},
-pages = {1445--1452},
-title = {{Similar Non-Random Processes Maintain Diversity in Two Tropical Rainforests}},
-url = {http://rspb.royalsocietypublishing.org/content/266/1427/1445},
-volume = {266},
-year = {1999}
-}
-@incollection{Marcon2012b,
-address = {Paris},
-author = {Marcon, Eric and Puech, Florence},
-booktitle = {D{\'{e}}veloppements r{\'{e}}cents en {\'{e}}conomie et finances internationales},
-editor = {Abdelmalki, Lahsen and Allegret, Jean-Pierre and Puech, Florence and Jallab, Mustapha Sadni and Silem, Ahmed},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech - 2012 - La mesure en {\'{e}}conomie internationale.pdf:pdf},
-pages = {15--27},
-publisher = {Armand Colin},
-title = {{La mesure en {\'{e}}conomie internationale}},
-year = {2012}
-}
-@article{Besag1977,
-abstract = {The Monte Carlo approach to testing a simple null hypothesis is reviewed briefly and several examples of its application to problems involving spatial distributions are presented. These include spatial point pattern, pattern similarity, space-time interaction and scales of pattern. The aim is not to present specific “recommended tests” but rather to illustrate the value of the general approach, particularly at a preliminary stage of analysis.},
-author = {Besag, Julian E. and Diggle, Peter J.},
-doi = {10.2307/2346974},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Besag, Diggle - 1977 - Simple Monte Carlo Tests for Spatial Pattern.pdf:pdf},
-journal = {Applied Statistics},
-number = {3},
-pages = {327--333},
-title = {{Simple Monte Carlo Tests for Spatial Pattern}},
-url = {http://www.jstor.org/stable/2346974},
-volume = {26},
-year = {1977}
-}
-@article{Willis2015,
-abstract = {We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors.},
-author = {Willis, Amy and Bunge, John},
-doi = {10.1111/biom.12332},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Willis, Bunge - 2015 - Estimating diversity via frequency ratios.pdf:pdf},
-journal = {Biometrics},
-number = {4},
-pages = {1042--1049},
-title = {{Estimating diversity via frequency ratios}},
-url = {http://doi.wiley.com/10.1111/biom.12332},
-volume = {71},
-year = {2015}
-}
-@article{Harte1999,
-abstract = {If the fraction of species in area A that are also found in one-half of that area is independent of A, the distribution of species is self-similar and a number of observed patterns in ecology, including the widely cited species-area relationship connecting species richness to censused area, follow. Self-similarity also leads to a species-abundance distribution, which deviates considerably from the commonly assumed Lognormal distribution and predicts considerably more rare species than the latter. Because the abundance distribution is derived under the condition of self-similarity, it:may be widely applicable beyond ecology.},
-author = {Harte, John and Kinzig, Ann and Green, Jessica},
-doi = {10.1126/science.284.5412.334},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harte, Kinzig, Green - 1999 - Self-similarity in the distribution and abundance of species.pdf:pdf},
-journal = {Science},
-number = {5412},
-pages = {334--336},
-title = {{Self-similarity in the distribution and abundance of species}},
-url = {http://science.sciencemag.org/content/284/5412/334},
-volume = {284},
-year = {1999}
-}
-@article{Ahrendsen2015,
-abstract = {Global biodiversity is declining rapidly as a consequence of anthropogenic changes to the environment. Traditional diversity indices such as species richness have been used to assess biodiversity, but recent arguments call for a more comprehensive assessment that includes both phylogenetic and functional diversity (PD and FD, respectively). Many PD metrics have been developed, but few empirical studies have compared metrics across sites with the goal of understanding their application to characterizing biodiversity. In this study, 17 PD metrics, four traditional diversity indices, and one measure of FD were calculated and compared between two Nebraska grasslands. PD metrics were calculated from robust phylogenies estimated from next-generation sequencing data of 45 species. Traditional indices were calculated using species abundance data, and FD was quantified by measuring the phylogenetic signal, K, of specific leaf area (SLA). Results showed that PD metrics and traditional indices were not always correlated, and various PD metrics characterized biodiversity differently. In addition, phylogenies estimated from {\textgreater}80 genes were more robust than single- or dual-gene phylogenies resulting in more reliable PD metrics. K of SLA indicated random trait assembly in all sites. Results suggested that metrics that identify phylogenetic structure and relatedness can provide information to conservation planners about the ability of a community to persist in an unpredictable future. A combination of these results with those of future investigations applying PD and FD metrics to varying communities will support concrete recommendations to conservation planners about how to incorporate these metrics into the selection of priority regions.},
-author = {Ahrendsen, Dakota L. and Aust, Shelly K. and {Roxanne Kellar}, P.},
-doi = {10.1007/s00606-015-1246-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ahrendsen, Aust, Roxanne Kellar - 2015 - Biodiversity assessment using next-generation sequencing comparison of phylogenetic and functio.pdf:pdf},
-journal = {Plant Systematics and Evolution},
-number = {1},
-pages = {89--108},
-title = {{Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands}},
-url = {http://link.springer.com/10.1007/s00606-015-1246-6},
-volume = {302},
-year = {2016}
-}
-@article{Qi2008,
-abstract = {Urban agglomeration (UA) compactness means spatial concentration degree of physical entities, such as cities (towns), industries, resources, funds, traffic and technologies, whose concentration is formed according to specified economic and technologic association in the process of UA formation and development. The UA industrial compactness means the concentration degree of industry and industry clusters with reference to the industrial, technological and economic relations among the cities in the UA in the process of rational industrial division and with the extension of industrial chain. After analyzing the researches on compactness, this paper finds that the relevant measurement coefficient and methods reflecting industrial geographical concentration fail to link industries spatial concentration with urban spatial concentration. Taking 23 UAs as samples and classifying them by development degree, this paper probes into UA compactness and spatial distribution characteristics from the perspective of industry by adopting UA index systems of industry and measurement models. The research finds out: 1) there is obvious positive correlation between UA industrial compactness and UA development degree; 2) the spatial distribution difference of UA industrial compactness is relatively great; and 3) UA industrial compactness shows a gradually decreasing tendency from the eastern part, the middle part to the western part of China. From the research thoughts and approaches, this article suggests that studies on the UA integrated compactness measurement should be enhanced from a multidimensional perspective involving space, traffic, population density and so on.},
-author = {Qi, Weifeng and Fang, Chuanglin and Song, Jitao},
-doi = {10.1007/s11769-008-0291-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Qi, Fang, Song - 2008 - Measurement and spatial distribution of urban agglomeration industrial compactness in China.pdf:pdf},
-journal = {Chinese Geographical Science},
-number = {4},
-pages = {291--299},
-title = {{Measurement and spatial distribution of urban agglomeration industrial compactness in China}},
-url = {http://dx.doi.org/10.1007/s11769-008-0291-2},
-volume = {18},
-year = {2008}
-}
-@article{Tuomisto2012,
-abstract = {Ecologists widely agree that species diversity consists of two components, richness (the number of species) and evenness (a measure of the equitability of the proportional abundances of those species). However, no consensus on an exact definition of evenness (or equitability) has emerged. Instead, numerous equitability indices have been used in the ecological literature, as different researchers have preferred indices with different mathematical properties. In this paper, I show that the phrase ‘species diversity consists of two independent components, richness and evenness' logically leads to one particular definition of evenness (Evenness = Diversity/Richness). To facilitate accurate communication, I propose that the term ‘evenness' be used only to refer to this phenomenon, and that other terms be used for the equitability indices that measure other things. Here I provide a review of popular equitability indices, explain what each measures in practice, and show how they relate to each other and to evenness itself. I also explore how the partitioning of diversity into richness and evenness components is related to the partitioning of diversity into alpha and beta components. Dissecting the indices makes it easier to see the conceptual differences among them. Such understanding is necessary to ensure that an appropriate index is chosen for the questions at hand, as well as to interpret the index values correctly and to assess when index values can and when they cannot be considered comparable.},
-author = {Tuomisto, Hanna},
-doi = {10.1111/j.1600-0706.2011.19897.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto - 2012 - An updated consumer's guide to evenness and related indices.pdf:pdf},
-journal = {Oikos},
-number = {8},
-pages = {1203--1218},
-title = {{An updated consumer's guide to evenness and related indices}},
-url = {http://dx.doi.org/10.1111/j.1600-0706.2011.19897.x},
-volume = {121},
-year = {2012}
-}
-@article{Maturo2017,
-abstract = {Humans are dependent on a large number of species of animals, plants, fungi, and microbes that provide indispensable ecosystem functions and produce essential goods. Apart from the economic valuation of the direct and indirect benefits of biodiversity, people place existence values on biodiversity, i.e. they consider the existence of particular species, regardless of the services they provide. There is also a general recognition that species diversity indicates the status of the ecosystem or community, and thus the quality of the living environment; hence, both at academic and institutional level, there is a lively discussion about how to properly measure and monitor biodiversity. Although many candidates have been proposed, nowadays, no scientific consensus measure exists, and this is mainly due to three motivations: the large number of properties that an indicator of biodiversity should meet, the definition of biodiversity, and the specific interests of policymakers or stakeholders that indicators should satisfy. Because most existing indices neglect the multivariate nature of biodiversity, we address this drawback by proposing a functional approach to Hill's numbers for assessing changes in species variety of ecological communities over time. New functional tools are developed, both analytical and graphical: we present “the biodiversity surface”, “the volume under the biodiversity surface”, and some indicators which have been derived from them. This functional multivariate approach provides additional tools to the existing biodiversity monitoring techniques, and allows us to address biodiversity by considering both richness and evenness, and all of their possible shades. The goal of this research is to provide policymakers, stakeholders, and scholars with additional tools for improving the understanding of biodiversity dynamics within ecological communities.},
-author = {Maturo, Fabrizio and {Di Battista}, Tonio},
-doi = {10.1016/j.ecolind.2017.08.016},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Maturo, Di Battista - 2017 - A functional approach to Hill's numbers for assessing changes in species variety of ecological communities.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {70--81},
-title = {{A functional approach to Hill's numbers for assessing changes in species variety of ecological communities over time}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X17304934},
-volume = {84},
-year = {2017}
-}
-@inproceedings{Goreaud2004,
-abstract = {The recent development of individual based and spatially explicit models raises the question of how to simulate relevant initial states for these models, and more particularly how to simulate realistic spatial structures. This is especially true for forest stand modelling. In this paper, we first review briefly the main simple steps in the simulation of forest stands with realistic spatial structure : (i) spatial structure analysis and ecological interpretation, (ii) expert simulation through classical point processes and ad hoc values of the parameters, and (iii) precise fitting of a spatial structure model using L(r) and L12(r) functions as criterion. We illustrate the advantages and limits of these steps on a real forest stand in mixed Oak - Scots pine forest near Orl{\'{e}}ans (France). We then propose a specific method - a mimetic point process - in order to simulate spatial structures similar to real patterns. This point process is based on a generalised Gibbs process, whose global cost function directly depends on the difference between the real measured values of L(r) and L12(r) functions, and the corresponding values computed on the simulated pattern at each iteration of the algorithm. We applied this method on a mixed Oak - Scots pine forest stand, and thus obtained an improved simulated pattern, that can be used as initial state for individual based forest growth models. We finally discuss the limits of this method, and its possible use to facilitate the valorisation of individual based models in the community of forest management. Keywords},
-address = {Paris},
-author = {Goreaud, Fran{\c{c}}ois and Loussier, B. and {Ngo Bieng}, Marie-Ange and Allain, R.},
-booktitle = {Interdisciplinary Spatial Statistics Workshop 2004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Goreaud et al. - 2004 - Simulating realistic spatial structure for forest stands a mimetic point process.pdf:pdf},
-title = {{Simulating realistic spatial structure for forest stands: a mimetic point process}},
-year = {2004}
-}
-@article{Hector2001,
-abstract = {The relationship between community diversity and invasion resistance in a grassland was examined using experimental plant assemblages that varied in species richness and composition. The assemblages were weeded for three seasons to remove unsown species and we used the number of weeded seedlings, their total biomass and the number of species removed as indicators of community resistance and susceptibility to invasion. In general, we found a positive relationship between invasion resistance and increasing community diversity. Similar patterns of establishment were observed at the end of the fourth field season after several months without weeding. Increased invasion resistance with higher diversity appears to come through reduced levels of several above- and below-ground resources, although these did not fully explain the effects of species richness in the study's analyses. Experimental increases and reductions of litter biomass within the study's experimental plant assemblages did not modify these patterns significantly. A review of comparable studies of invasion across directly manipulated diversity gradients revealed similar patterns. Positive effects of species diversity on invasion resistance were found in experimental manipulations of plant diversity conducted in the field and in the glasshouse, from studies with aquatic microcosms and in a marine system. Although some exceptions to this pattern were found in both terrestrial plant systems and aquatic microcosms, it was concluded that in biodiversity manipulation experiments more diverse communities are generally more resistant to invasion.},
-author = {Hector, Andrew and Dobson, Kim and Minns, Asher and Bazeley-White, Ellen and Lawton, John Hartley},
-doi = {10.1046/j.1440-1703.2001.00443.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hector et al. - 2001 - Community diversity and invasion resistance An experimental test in a grassland ecosystem and a review of compara.pdf:pdf},
-journal = {Ecological Research},
-number = {5},
-pages = {819--831},
-title = {{Community diversity and invasion resistance: An experimental test in a grassland ecosystem and a review of comparable studies}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1440-1703.2001.00443.x/abstract},
-volume = {16},
-year = {2001}
-}
-@article{Cao2010,
-abstract = {1. Similarity indices are commonly used for multivariate analyses, estimations of $\beta$-diversity and assessments of ecological impacts of disturbances. Both statistical and ecological criteria have guided index selections. The former criteria includes accuracy (i.e. how close an estimate is to the true value) and precision (i.e. how repeatable different estimates are) while the latter is focused on detection of known assemblage changes or environmental gradients. 2. These two types of criteria, however, often lead to conflicting recommendations of similarity indices. We hypothesized that a key statistical criterion, accuracy, is either irrelevant or incompatible with the ecological criteria. 3. To test this hypothesis, we compared eight commonly used similarity indices for quantifying the responses of stream macroinvertebrate assemblages to a simulated stress gradient based on both types of criteria. 4. Chao's abundance-based Jaccard and S{\o}renson coefficients, and Morisita index were most accurate but strongly nonlinear in response to linear community changes and the least or less capable of discriminating stress levels. By comparison, the Bray–Curtis index, CY similarity index and Canberra Metric were less or least accurate, but outperformed the first three indices in all ecological criteria used. Multiple linear regressions confirmed that accuracy is irrelevant to or incompatible with the ecological criteria. 5. Synthesis and applications. By examining the relationships between the statistical and ecological performances of similarity indices, our study provides a critical synthesis of index evaluations and clarified much existing confusion about index selection.},
-author = {Cao, Yong and Epifanio, John},
-doi = {10.1111/j.2041-210X.2010.00040.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cao, Epifanio - 2010 - Quantifying the responses of macroinvertebrate assemblages to simulated stress are more accurate similarity indic.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {4},
-pages = {380--388},
-title = {{Quantifying the responses of macroinvertebrate assemblages to simulated stress: are more accurate similarity indices less useful?}},
-url = {http://doi.wiley.com/10.1111/j.2041-210X.2010.00040.x},
-volume = {1},
-year = {2010}
-}
-@article{Hardy2008a,
-abstract = {1. Analyzing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species. For instance, an association between species co-occurrence in local communities and their phylogenetic proximity may reveal the action of habitat filtering, niche conservatism and/or competitive exclusion. 2. Different methods were recently proposed to test such community-wide phylogenetic patterns, based on the phylogenetic clustering or overdispersion of the species in a local community. This provides a much needed framework for addressing long standing questions in community ecology as well as the recent debate on community neutrality. The testing procedures are based on (i) a metric measuring the association between phylogenetic distance and species co-occurrence, and (ii) a data set randomization algorithm providing the distribution of the metric under a given 'null model'. However, the statistical properties of these approaches are not well-established and their reliability must be tested against simulated data sets. 3. This paper reviews metrics and null models used in previous studies. A 'locally neutral' subdivided community model is simulated to produce data sets devoid of phylogenetic structure in the spatial distribution of species. Using these data sets, the consistency of Type I error rates of tests based on 10 metrics combined with nine null models is examined. 4. This study shows that most tests can become liberal (i.e. tests rejecting too often the null hypothesis that only neutral processes structured spatially the local community) when the randomization algorithm breaks down a structure in the original data set unrelated to the null hypothesis to test. Hence, when overall species abundances are distributed non-randomly across the phylogeny or when local abundances are spatially autocorrelated, better statistical performances were achieved by randomization algorithms preserving these structural features. The most reliable randomization algorithm consists of permuting species with similar abundances among the tips of the phylogenetic tree. One metric, R(PD-DO), also proved to be robust under most simulated conditions using a variety of null models. 5. Synthesis. Given the suboptimal performances of several tests, attention must be paid to the testing procedures used in future studies. Guidelines are provided to help choosing an adequate test.},
-annote = {ISI Document Delivery No.: 336QN
-Times Cited: 61
-Cited Reference Count: 39
-Hardy, Olivier J.
-Wiley-blackwell
-Malden},
-author = {Hardy, Olivier J.},
-doi = {10.1111/j.1365-2745.2008.01421.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hardy - 2008 - Testing the spatial phylogenetic structure of local communities statistical performances of different null models and tes.pdf:pdf},
-journal = {Journal of Ecology},
-number = {5},
-pages = {914--926},
-title = {{Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2008.01421.x/full},
-volume = {96},
-year = {2008}
-}
-@article{Thompson2017,
-author = {Thompson, J N and Cunningham, B.M.2002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thompson, Cunningham - 2017 - Geographic structure and dynamics of coevolutionary selection.pdf:pdf},
-journal = {Nature},
-number = {1997},
-pages = {735--738},
-title = {{Geographic structure and dynamics of coevolutionary selection}},
-url = {e:{\%}5CLUCAS FIORELLI{\%}5CBDD022-0325.pdf},
-volume = {417(6890)},
-year = {2017}
-}
-@article{Cheng2013,
-abstract = {Precise characterization of hydroclimate variability in Amazonia on various timescales is critical to understanding the link between climate change and biodiversity. Here we present absolute-dated speleothem oxygen isotope records that characterize hydroclimate variation in western and eastern Amazonia over the past 250 and 20 ka, respectively. Although our records demonstrate the coherent millennial-scale precipitation variability across tropical-subtropical South America, the orbital-scale precipitation variability between western and eastern Amazonia exhibits a quasi-dipole pattern. During the last glacial period, our records imply a modest increase in precipitation amount in western Amazonia but a significant drying in eastern Amazonia, suggesting that higher biodiversity in western Amazonia, contrary to 'Refugia Hypothesis', is maintained under relatively stable climatic conditions. In contrast, the glacial-interglacial climatic perturbations might have been instances of loss rather than gain in biodiversity in eastern Amazonia, where forests may have been more susceptible to fragmentation in response to larger swings in hydroclimate.},
-archivePrefix = {arXiv},
-arxivId = {DOI: 10.1038/ncomms2415},
-author = {Cheng, Hai and Sinha, Ashish and Cruz, Francisco W. and Wang, Xianfeng and Edwards, R. Lawrence and D'Horta, Fernando M. and Ribas, Camila C. and Vuille, Mathias and Stott, Lowell D. and Auler, Augusto S.},
-doi = {10.1038/ncomms2415},
-eprint = {ncomms2415},
-isbn = {2041-1723},
-issn = {20411723},
-journal = {Nature Communications},
-pmid = {23361002},
-primaryClass = {DOI: 10.1038},
-title = {{Climate change patterns in Amazonia and biodiversity}},
-volume = {4},
-year = {2013}
-}
-@book{Isard1960,
-author = {Isard, Walter},
-publisher = {MIT Press},
-title = {{Methods of Regional Analysis}},
-year = {1960}
-}
-@book{Hoover1948,
-address = {New York},
-author = {Hoover, Edgar M.},
-publisher = {McGraw-Hill},
-title = {{The Location of Economic Activity}},
-year = {1948}
-}
-@article{Bluthgen2006,
-abstract = {BACKGROUND: Network analyses of plant-animal interactions hold valuable biological information. They are often used to quantify the degree of specialization between partners, but usually based on qualitative indices such as 'connectance' or number of links. These measures ignore interaction frequencies or sampling intensity, and strongly depend on network size. RESULTS: Here we introduce two quantitative indices using interaction frequencies to describe the degree of specialization, based on information theory. The first measure (d') describes the degree of interaction specialization at the species level, while the second measure (H2') characterizes the degree of specialization or partitioning among two parties in the entire network. Both indices are mathematically related and derived from Shannon entropy. The species-level index d' can be used to analyze variation within networks, while H2' as a network-level index is useful for comparisons across different interaction webs. Analyses of two published pollinator networks identified differences and features that have not been detected with previous approaches. For instance, plants and pollinators within a network differed in their average degree of specialization (weighted mean d'), and the correlation between specialization of pollinators and their relative abundance also differed between the webs. Rarefied sampling effort in both networks and null model simulations suggest that H2' is not affected by network size or sampling intensity. CONCLUSION: Quantitative analyses reflect properties of interaction networks more appropriately than previous qualitative attempts, and are robust against variation in sampling intensity, network size and symmetry. These measures will improve our understanding of patterns of specialization within and across networks from a broad spectrum of biological interactions.},
-author = {Bl{\"{u}}thgen, Nico and Menzel, Florian and Bl{\"{u}}thgen, Nils},
-doi = {10.1186/1472-6785-6-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bl{\"{u}}thgen, Menzel, Bl{\"{u}}thgen - 2006 - Measuring specialization in species interaction networks.pdf:pdf},
-journal = {BMC Ecology},
-pages = {9},
-title = {{Measuring specialization in species interaction networks.}},
-url = {http://bmcecol.biomedcentral.com/articles/10.1186/1472-6785-6-9},
-volume = {6},
-year = {2006}
-}
-@article{McGill2006,
-abstract = {There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.},
-author = {McGill, Brian J. and Enquist, Brian J. and Weiher, Evan and Westoby, Mark},
-doi = {10.1016/j.tree.2006.02.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McGill et al. - 2006 - Rebuilding community ecology from functional traits.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {4},
-pages = {178--85},
-title = {{Rebuilding community ecology from functional traits}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/16701083},
-volume = {21},
-year = {2006}
-}
-@article{Marcon2014a,
-abstract = {Traditional measures of diversity, namely the number of species as well as Simpson's and Shannon's indices, are particular cases of Tsallis entropy. Entropy decomposition, i.e. decomposing gamma entropy into alpha and beta components, has been previously derived in the literature. We propose a generalization of the additive decomposition of Shannon entropy applied to Tsallis entropy. We obtain a self-contained definition of beta entropy as the information gain brought by the knowledge of each community composition. We propose a correction of the estimation bias allowing to estimate alpha, beta and gamma entropy from the data and eventually convert them into true diversity. We advocate additive decomposition in complement of multiplicative partitioning to allow robust estimation of biodiversity.},
-author = {Marcon, Eric and Scotti, Ivan and H{\'{e}}rault, Bruno and Rossi, Vivien and Lang, Gabriel},
-doi = {10.1371/journal.pone.0090289},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon et al. - 2014 - Generalization of the Partitioning of Shannon Diversity.pdf:pdf},
-journal = {Plos One},
-number = {3},
-pages = {e90289},
-title = {{Generalization of the Partitioning of Shannon Diversity}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090289},
-volume = {9},
-year = {2014}
-}
-@article{Feser2001,
-abstract = {This paper uses the inverse input demand function framework of Kim [Review of Economics and Statistics, 74 (1992) 546–551] to test for economies of industry and urban size in two US manufacturing sectors of differing technology intensity: farm and garden machinery (SIC 352) and measuring and controlling devices (SIC 382). The inverse input demand framework permits the estimation of the production function jointly with a set of cost shares without the imposition of prior economic restrictions. Tests using plant-level data suggest the presence of population scale (urbanization) economies in the moderate- to low-technology farm and garden machinery sector and industry scale (localization) economies in the higher technology measuring and controlling devices sector. The efficiency and generality of the inverse input demand approach are particularly appropriate for micro-level studies of agglomeration economies where prior assumptions regarding homogeneity and homotheticity are less appropriate.},
-author = {Feser, Edward J.},
-doi = {10.1016/S0166-0462(00)00057-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser - 2001 - A flexible test for agglomeration economies in two US manufacturing industries.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {7},
-pages = {1--19},
-title = {{A flexible test for agglomeration economies in two US manufacturing industries}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046200000570},
-volume = {31},
-year = {2001}
-}
-@article{Ruiz2012,
-abstract = {Comparison of thematic maps is an important task in a number of disciplines. Map comparison has traditionally been conducted using cell-by-cell agreement indicators. More recently, other methods have been proposed that take into account not only spatially coincident cells in two maps, but also their surroundings or the spatial structure of their differences. The objective of this article is to propose a framework for map comparison that considers (1) the patterns of spatial association in two maps, in other words, the map elements in their surroundings; (2) the equivalence of those patterns; and (3) the independence of patterns between maps. Two new statistics for the spatial analysis of qualitative data are introduced that are based on the symbolic entropy of the maps. As well, all inferential elements to conduct hypothesis testing are developed. The framework is illustrated using real and simulated maps.},
-annote = {ISI Document Delivery No.: 897JE
-Times Cited: 0
-Cited Reference Count: 44
-Ruiz, Manuel Lopez, Fernando Paez, Antonio
-MCINN (Ministerio de Ciencia e Innovacion)[MTM2009-07373]; Fundacion Seneca of Region de Murcia; Social Sciences and Humanities Research Council of Canada[861-2009-2010]; Ministerio de Ciencia y Tecnologia[ECO-2009-10534-ECON]; Fundacion Seneca de la Region de Murcia[11897/PHCS/09]
-The authors gratefully acknowledge the feedback of five anonymous reviewers who commented on two early versions of this article. Manuel Ruiz Mairn was partially supported by MCINN (Ministerio de Ciencia e Innovacion) grant MTM2009-07373, Fundacion Seneca of Region de Murcia, and by grant 861-2009-2010 from the Social Sciences and Humanities Research Council of Canada. Fernando Lopez received financial support from project ECO-2009-10534-ECON of Ministerio de Ciencia y Tecnologia and from project 11897/PHCS/09 of Fundacion Seneca de la Region de Murcia.
-Taylor {\&} francis ltd
-Abingdon},
-author = {Ruiz, M and Lopez, F and Paez, A},
-doi = {10.1080/13658816.2011.586327},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ruiz, Lopez, Paez - 2012 - Comparison of thematic maps using symbolic entropy.pdf:pdf},
-journal = {International Journal of Geographical Information Science},
-number = {3},
-pages = {413--439},
-title = {{Comparison of thematic maps using symbolic entropy}},
-volume = {26},
-year = {2012}
-}
-@article{Diggle1977,
-abstract = {The author's earlier analytical results on the robustness of distance-based estimators of density are supplemented by a simulation study, with particular attention being given to various types of aggregated spatial point patterns. In addition, some remarks on heterogeneous patterns are made. Finally, the results of an application to data on tree locations are described.},
-author = {Diggle, Peter J.},
-doi = {10.1093/biomet/64.1.91},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle - 1977 - A note on robust density estimation for spatial point patterns.pdf:pdf},
-journal = {Biometrika},
-number = {1},
-pages = {91--95},
-title = {{A note on robust density estimation for spatial point patterns}},
-url = {https://academic.oup.com/biomet/article-abstract/64/1/91/515815/A-note-on-robust-density-estimation-for-spatial},
-volume = {64},
-year = {1977}
-}
-@article{Good1956,
-abstract = {A sample of size N is drawn at random from a population of animals of various species. Methods are given for estimating, knowing only the contents of this sample, the number of species which will be represented r times in a second sample of size {\{}lambda{\}}N; these also enable us to estimate the number of different species and the proportion of the whole population represented in the second sample. A formula is found for the variance of the estimate; when A{\textgreater}2, this variance becomes in general very large, so that the estimate is useless without some modification. This difficulty can be partly overcome, at least for A{\textless}5, by using Euler's method with a suitable parameter or the methods described by Shanks (1955) to hasten the convergence of the series by which the estimate is expressed. The methods are applied to samples of words from Our Mutual Friend, to an entomological sample, and to a sample of nouns from Macaulay's essay on Bacon.},
-author = {Good, I. J. and Toulmin, G. H.},
-doi = {10.1093/biomet/43.1-2.45},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Good, Toulmin - 1956 - The Number of new species, and the increase in population coverage, when a sample is increased.pdf:pdf},
-journal = {Biometrika},
-number = {1-2},
-pages = {45--63},
-title = {{The Number of new species, and the increase in population coverage, when a sample is increased}},
-url = {http://biomet.oxfordjournals.org/cgi/content/abstract/43/1-2/45},
-volume = {43},
-year = {1956}
-}
-@article{Guiasu2012,
-author = {Guiasu, Radu Cornel and Guiasu, Silviu},
-doi = {10.1155/2012/478728},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guiasu, Guiasu - 2012 - The Weighted Gini-Simpson Index Revitalizing an Old Index of Biodiversity.pdf:pdf},
-issn = {1687-9708},
-journal = {International Journal of Ecology},
-number = {478728},
-pages = {1--10},
-title = {{The Weighted Gini-Simpson Index: Revitalizing an Old Index of Biodiversity}},
-url = {http://www.hindawi.com/journals/ijecol/2012/478728/},
-volume = {2012},
-year = {2012}
-}
-@article{Aubry-Kientz2013,
-abstract = {Tree mortality in tropical forests is a complex ecological process for which modelling approaches need to be improved to better understand, and then predict, the evolution of tree mortality in response to global change. The mortality model introduced here computes an individual probability of dying for each tree in a community. The mortality model uses the ontogenetic stage of the tree because youngest and oldest trees are more likely to die. Functional traits are integrated as proxies of the ecological strategies of the trees to permit generalization among all species in the community. Data used to parametrize the model were collected at Paracou study site, a tropical rain forest in French Guiana, where 20,408 trees have been censused for 18 years. A Bayesian framework was used to select useful covariates and to estimate the model parameters. This framework was developed to deal with sources of uncertainty, including the complexity of the mortality process itself and the field data, especially historical data for which taxonomic determinations were uncertain. Uncertainty about the functional traits was also considered, to maximize the information they contain. Four functional traits were strong predictors of tree mortality: wood density, maximum height, laminar toughness and stem and branch orientation, which together distinguished the light-demanding, fast-growing trees from slow-growing trees with lower mortality rates. Our modelling approach formalizes a complex ecological problem and offers a relevant mathematical framework for tropical ecologists to process similar uncertain data at the community level.},
-annote = {Mod{\`{e}}le d'attribution d'une probabilit{\'{e}} d'esp{\`{e}}ce {\`{a}} un nom vernaculaire en annexe 2.},
-author = {Aubry-Kientz, M{\'{e}}laine and H{\'{e}}rault, Bruno and Ayotte-Tr{\'{e}}panier, Charles and Baraloto, Christopher and Rossi, Vivien},
-doi = {10.1371/journal.pone.0063678},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Aubry-Kientz et al. - 2013 - Toward Trait-Based Mortality Models for Tropical Forests.pdf:pdf},
-journal = {PLoS ONE},
-number = {5},
-pages = {e63678},
-title = {{Toward Trait-Based Mortality Models for Tropical Forests}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063678},
-volume = {8},
-year = {2013}
-}
-@techreport{Midelfart-Knarvik2000,
-abstract = {The objectives of this study are to describe the changes in industrial location that have occured in Europe in recent decades; to establish whether these are associated with countries' economic structures becoming more or less similar, and industries becoming more or less spatially concentrated; to compare industrial location patterns in Europe and the US; and to identify the underlying forces that determine industrial location and assess the extent to which these have changed in recent years.},
-address = {Brussels},
-author = {Midelfart-Knarvik, Karen Helene and Overman, Henry G. and Redding, Stephen J. and Venables, Anthony J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Midelfart-Knarvik et al. - 2000 - The Location of European Industry.pdf:pdf},
-publisher = {European Commission},
-title = {{The Location of European Industry}},
-url = {http://ec.europa.eu/economy{\_}finance/publications/pages/publication{\_}summary11139{\_}en.htm},
-year = {2000}
-}
-@article{Newman2004,
-abstract = {We propose and study a set of algorithms for discovering community structure in networks -- natural divisions of network nodes into densely connected subgroups. Our algorithms all share two definitive features: first, they involve iterative removal of edges from the network to split it into communities, the edges removed being identified using one of a number of possible "betweenness" measures, and second, these measures are, crucially, recalculated after each removal. We also propose a measure for the strength of the community structure found by our algorithms, which gives us an objective metric for choosing the number of communities into which a network should be divided. We demonstrate that our algorithms are highly effective at discovering community structure in both computer-generated and real-world network data, and show how they can be used to shed light on the sometimes dauntingly complex structure of networked systems.},
-author = {Newman, M. E. J. and Girvan, M.},
-doi = {10.1103/PhysRevE.69.026113},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Newman, Girvan - 2004 - Finding and evaluating community structure in networks.pdf:pdf},
-journal = {Physical Review E},
-number = {2},
-pages = {026113},
-title = {{Finding and evaluating community structure in networks}},
-url = {http://arxiv.org/abs/cond-mat/0308217 http://dx.doi.org/10.1103/PhysRevE.69.026113},
-volume = {69},
-year = {2004}
-}
-@article{Ripley1978a,
-abstract = {(1) Spectral analysis is a relatively untried method for the analysis of data from a line of contiguous quadrats. Conventional block-size analyses are shown to be related to square waves. In spectral analysis square waves are replaced by sine waves. (2) These methods and Mead's test are compared with conventional methods, using artificial and field data. Spectral analysis performed reliably and gave a good indication of the type of departure from a random pattern. Mead's test proved sensitive but hard to interpret, often contradicting other methods. (3) It is argued that standardization should not be used with methods based on variances.},
-author = {Ripley, Brian D.},
-doi = {10.2307/2259308},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1978 - Spectral Analysis and the Analysis of Pattern in Plant Communities.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {965--981},
-title = {{Spectral Analysis and the Analysis of Pattern in Plant Communities}},
-url = {https://www.jstor.org/stable/2259308},
-volume = {66},
-year = {1978}
-}
-@article{Pavoine2008,
-abstract = {Abouheif adapted a test for serial. independence to detect a phylogenetic signal in phenotypic traits. We provide the exact analytic value of this test, revealing that it uses Moran's I statistic with a new matrix of phylogenetic proximities. We introduce then two new matrices of phylogenctic proximities highlighting their mathematical properties: matrix A which is used in Abouheif test and matrix M which is related to A and biodiversity studies. Matrix A unifies the tests developed by Abouheif, Moran and Geary. We discuss the advantages of matrices A and M over three widely used phylogenetic proximity matrices through simulations evaluating power and type-I error of tests for phylogenetic autocorrelation. We conclude that A enhances the power of Moran's test and is useful for unresolved trees. Data sets and routines are freely available in an online package and explained in an online supplementary file. (C) 2007 Elsevier Inc. All rights reserved.},
-author = {Pavoine, Sandrine and Ollier, S{\'{e}}bastien and Pontier, Dominique and Chessel, Daniel},
-doi = {10.1016/j.tpb.2007.10.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2008 - Testing for phylogenetic signal in phenotypic traits New matrices of phylogenetic proximities.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {1},
-pages = {79--91},
-title = {{Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities}},
-volume = {73},
-year = {2008}
-}
-@article{Scholes2005,
-abstract = {The nations of the world have set themselves a target of reducing the rate of biodiversity loss by 2010. Here, we propose a biodiversity intactness index (BII) for assessing progress towards this target that is simple and practical--but sensitive to important factors that influence biodiversity status--and which satisfies the criteria for policy relevance set by the Convention on Biological Diversity. Application of the BII is demonstrated on a large region (4 x 10(6) km2) of southern Africa. The BII score in the year 2000 is about 84{\%}: in other words, averaged across all plant and vertebrate species in the region, populations have declined to 84{\%} of their presumed pre-modern levels. The taxonomic group with the greatest loss is mammals, at 71{\%} of pre-modern levels, and the ecosystem type with the greatest loss is grassland, with 74{\%} of its former populations remaining. During the 1990s, a population decline of 0.8{\%} is estimated to have occurred.},
-author = {Scholes, R. J. and Biggs, R.},
-doi = {10.1038/nature03289},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scholes, Biggs - 2005 - A Biodiversity Intactness Index.pdf:pdf},
-journal = {Nature},
-number = {7029},
-pages = {45--49},
-title = {{A Biodiversity Intactness Index}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/15744293},
-volume = {434},
-year = {2005}
-}
-@article{Gaston2000,
-abstract = {To a first approximation, the distribution of biodiversity across the Earth can be described in terms of a relatively small number of broad-scale spatial patterns. Although these patterns are increasingly well documented, understanding why they exist constitutes one of the most significant intellectual challenges to ecologists and biogeographers. Theory is, however, developing rapidly, improving in its internal consistency, and more readily subjected to empirical challenge. iodiversity,},
-annote = {10.1038/35012228},
-author = {Gaston, Kevin J.},
-doi = {10.1038/35012228},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gaston - 2000 - Global patterns in biodiversity.pdf:pdf},
-journal = {Nature},
-number = {6783},
-pages = {220--227},
-title = {{Global patterns in biodiversity}},
-url = {http://dx.doi.org/10.1038/35012228},
-volume = {405},
-year = {2000}
-}
-@article{Besag1989,
-abstract = {Simple Monte Carlo significance testing has many applications, particularly in the preliminary analysis of spatial data. The method requires the value of the test statistic to be ranked among a random sample of values generated according to the null hypothesis. However, there are situations in which a sample of values can only be conveniently generated using a Markov Chain, initiated by the observed data, so that independence is violated. This paper describes two methods that overcome the problem of dependence and allow exact tests to be carried out. The methods are applied to the Rasch model, to the finite lattice Ising model and to the testing of association between spatial processes. Power is discussed in a simple case.},
-author = {Besag, Julian E. and Clifford, Peter},
-doi = {10.2307/2336623},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Besag, Clifford - 1989 - Generalized Monte Carlo Significance Tests.pdf:pdf},
-journal = {Biometrika},
-number = {4},
-pages = {633--642},
-title = {{Generalized Monte Carlo Significance Tests}},
-url = {https://www.jstor.org/stable/2336623},
-volume = {76},
-year = {1989}
-}
-@article{Patil1982,
-abstract = {This paper puts forth the view that diversity is an average property of a community and identifies that property as species rarity. An intrinsic diversity ordering of communities is defined and is shown to be equivalent to stochastic ordering. Also, the sensitivity of an index to rare species is developed, culminating in a crossing-point theorem and a response theory to perturbations. Diversity decompositions, analogous to the analysis of variance, are discussed for two-way classifications and mixtures. The paper concludes with a brief survey of genetic diversity, linguistic diversity, industrial concentration, and income inequality.},
-author = {Patil, Ganapati P. and Taillie, Charles},
-doi = {10.2307/2287709},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Patil, Taillie - 1982 - Diversity as a concept and its measurement.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {379},
-pages = {548--561},
-title = {{Diversity as a concept and its measurement}},
-url = {https://www.jstor.org/stable/2287709},
-volume = {77},
-year = {1982}
-}
-@article{VanBuuren2006,
-abstract = {The use of the Gibbs sampler with fully conditionally specified models, where the distribution of each variable given the other variables is the starting point, has become a popular method to create imputations in incomplete multivariate data. The theoretical weakness of this approach is that the specified conditional densities can be incompatible, and therefore the stationary distribution to which the Gibbs sampler attempts to converge may not exist. This study investigates practical consequences of this problem by means of simulation. Missing data are created under four different missing data mechanisms. Attention is given to the statistical behavior under compatible and incompatible models. The results indicate that multiple imputation produces essentially unbiased estimates with appropriate coverage in the simple cases investigated, even for the incompatible models. Of particular interest is that these results were produced using only five Gibbs iterations starting from a simple draw from observed marginal distributions. It thus appears that, despite the theoretical weaknesses, the actual performance of conditional model specification for multivariate imputation can be quite good, and therefore deserves further study. Keywords:},
-author = {van Buuren, Stef and Brand, J. P. L. and Groothuis-Oudshoorn, C. G. M. and Rubin, D. B.},
-doi = {10.1080/10629360600810434},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/van Buuren et al. - 2006 - Fully conditional specification in multivariate imputation.pdf:pdf},
-journal = {Journal of Statistical Computation and Simulation},
-number = {12},
-pages = {1049--1064},
-title = {{Fully conditional specification in multivariate imputation}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/10629360600810434},
-volume = {76},
-year = {2006}
-}
-@article{Rajaram2016,
-abstract = {This paper is part of a series addressing the empirical/statistical distribution of the diversity of complexity within and amongst complex systems. Here, we consider the problem of measuring the diversity of complexity in a system, given its ordered range of complexity types i and their probability of occurrence pi, with the understanding that larger values of i mean a higher degree of complexity. To address this problem, we introduce a new complexity measure called case-based entropy Cc - a modification of the Shannon-Wiener entropy measure H. The utility of this measure is that, unlike current complexity measures-which focus on the macroscopic complexity of a single system - Cc can be used to empirically identify and measure the distribution of the diversity of complexity within and across multiple natural and human-made systems, as well as the diversity contribution of complexity of any part of a system, relative to the total range of ordered complexity types.},
-author = {Rajaram, R. and Castellani, B.},
-doi = {10.1016/j.physa.2016.02.007},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rajaram, Castellani - 2016 - An entropy based measure for comparing distributions of complexity.pdf:pdf},
-journal = {Physica A: Statistical Mechanics and its Applications},
-pages = {35--43},
-title = {{An entropy based measure for comparing distributions of complexity}},
-url = {http://dx.doi.org/10.1016/j.physa.2016.02.007},
-volume = {453},
-year = {2016}
-}
-@article{Lavorel2008,
-abstract = {Interpreting the functional diversity of vegetation is important in unravelling the relationship between environmental change, community composition and ecosystem processes. Functional diversity is the range and distribution of functional trait values in a community. It can be described, among other indicators, by community-level weighted means of trait values (CWM) and functional divergence. Standard methods exist for trait measurements but not for assessments of CWM and functional divergence in the field. No research has addressed the effects of different methods of estimating relative abundances, nor the need to estimate traits at individual, population or species level, or whether methods could be used that bypass taxonomy all together. This study reviews and evaluates plot-level assessment methods of functional diversity in herbaceous vegetation. We asked: (i) Should the objective of the study influence the method for estimating relative abundance? (ii) What are the strengths and limitations of intensive vs. 'rapid' approaches, and when should either be applied? (iii) Are taxon-free methods robust in comparison to taxon-explicit methods of trait measurement? Under what circumstances might they be applied? Our review of published studies that have measured functional diversity in the field showed that the choice of metric has not generally taken into account the link between the metric and the functions of interest, and that vegetation cover has been most widely used, regardless of study purpose. We compared quantitatively in subalpine grasslands three methods for quantification of species abundances plus one taxon-free method. We found that: (i) data base trait values were robust across years for a diverse set of dominant species; (ii) CWM have little sensitivity to method for estimating relative abundances; this sensitivity also depends on traits, for example, seed mass results were less stable than leaf traits and heights; (iii) robust estimates of CWM were obtained from visual estimates of species ranks and biomass using a dry-weight ranking method (BOTANAL), whereas functional divergence was more sensitive to method; and (iv) the taxon-free method should be treated with more caution and performed particularly poorly for estimates of functional divergence. We conclude that methodology can affect estimates of functional diversity. Although care should be taken in the choice of method and interpretation of results, rapid methods often offer promising avenues for sampling larger areas and/or repeated measures.},
-author = {Lavorel, Sandra and Grigulis, Karl and McIntyre, Sue and Williams, N. S. G. and Garden, Denys and Dorrough, Josh and Berman, Sandra and Qu{\'{e}}tier, Fabien and Th{\'{e}}bault, Aur{\'{e}}lie and Bonis, Anne},
-doi = {10.1111/j.1365-2435.2007.01339.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lavorel et al. - 2008 - Assessing functional diversity in the field - Methodology matters!.pdf:pdf},
-journal = {Functional Ecology},
-pages = {134--147},
-title = {{Assessing functional diversity in the field - Methodology matters!}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2007.01339.x/full},
-volume = {22},
-year = {2008}
-}
-@article{Heltshe1983,
-abstract = {An exact expression is given for the jackknife estimate of the number of species in a community and for the variance of this number when quadrat sampling procedures are used. The jackknife estimate is a function of the number of species that occur in one and only one quadrat. The variance of the number of species can be constructed, as can approximate two-sided confidence intervals. The behavior of the jackknife estimate, as affected by quadrat size, sample size and sampling area, is investigated by simulation.},
-author = {Heltshe, James F. and Forrester, Nancy E.},
-doi = {10.2307/2530802},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Heltshe, Forrester - 1983 - Estimating species richness using the jackknife procedure.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {1--11},
-title = {{Estimating species richness using the jackknife procedure}},
-url = {http://www.jstor.org/stable/2530802},
-volume = {39},
-year = {1983}
-}
-@book{Barbour1987,
-author = {Barbour, M. G. and Burk, J. H. and Pitts, W. D.},
-isbn = {9780805305418},
-publisher = {Benjamin/Cummings Pub. Co.},
-title = {{Terrestrial plant ecology}},
-url = {http://books.google.fr/books?id=Ip3wAAAAMAAJ},
-year = {1987}
-}
-@article{Feeley2011a,
-abstract = {Long-term studies have revealed that the structure and dynamics of many tropical forests are changing, but the causes and consequences of these changes remain debated. To learn more about the forces driving changes within tropical forests, we investigated shifts in tree species composition over the past 25 years within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, and examined how observed patterns relate to predictions of (1) random population fluctuations, (2) carbon fertilization, (3) succession from past disturbance, (4) recovery from an extreme El Ni{\~{n}}o drought at the start of the study period, and (5) long-term climate change. We found that there have been consistent and directional changes in the tree species composition. These shifts have led to increased relative representations of drought-tolerant species as determined by the species' occurrence both across a gradient of soil moisture within BCI and across a wider precipitation gradient from a dry forest near the Pacific coast of Panama to a wet forest near its Caribbean coast. These nonrandom changes cannot be explained by stochastic fluctuations or carbon fertilization. They may be the legacy of the El Ni{\~{n}}o drought, or alternatively, potentially reflect increased aridity due to long-term climate change. By investigating compositional changes, we increased not only our understanding of the ecology of tropical forests and their responses to large-scale disturbances, but also our ability to predict how future global change will impact some of the critical services provided by these important ecosystems.},
-author = {Feeley, Kenneth J. and Davies, Stuart J. and Perez, Rolando and Hubbell, Stephen P. and Foster, Robin B.},
-doi = {10.1890/10-0724.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feeley et al. - 2011 - Directional changes in the species composition of a tropical forest.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {871--82},
-title = {{Directional changes in the species composition of a tropical forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/10-0724.1/full},
-volume = {92},
-year = {2011}
-}
-@article{Diaz2001a,
-abstract = {The links between plant diversity and ecosystem functioning remain highly controversial. There is a growing consensus, however, that functional diversity, or the value and range of species traits, rather than species numbers per se, strongly determines ecosystem functioning. Despite its importance, and the fact that species diversity is often an inadequate surrogate, functional diversity has been studied in relatively few cases. Approaches based on species richness on the one hand, and on functional traits and types on the other, have been extremely productive in recent years, but attempts to connect their findings have been rare. Crossfertilization between these two approaches is a promising way of gaining mechanistic insight into the links between plant diversity and ecosystem processes and contributing to practical management for the conservation of diversity and ecosystem services.},
-author = {D{\'{i}}az, Sandra and Cabido, Marcelo},
-doi = {10.1016/S0169-5347(01)02283-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diaz, Cabido - 2001 - Vive la difference plant functional diversity matters to ecosystem processes.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {11},
-pages = {646--655},
-title = {{Vive la difference: plant functional diversity matters to ecosystem processes}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534701022832},
-volume = {16},
-year = {2001}
-}
-@article{Molino2001,
-abstract = {The “intermediate disturbance hypothesis”, which postulates maximum diversity at intermediate regimes of disturbance, has never been clearly proved to apply to species-rich tropical forest tree communities and to local-scale canopy disturbances that modify light environments. This hypothesis was tested on a sample of 17,000 trees in a Guianan forest, 10 years after a silvicultural experiment that added to natural treefall gaps a wide range of disturbance intensities. Species richness, standardized to eliminate density effects, peaked at intermediate disturbance levels, particularly when disturbance intensity was estimated through the percentage of stems of strongly light-dependent species.},
-author = {Molino, Jean-Fran{\c{c}}ois and Sabatier, Daniel},
-doi = {10.1126/science.1060284},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Molino, Sabatier - 2001 - Tree diversity in tropical rain forests a validation of the intermediate disturbance hypothesis.pdf:pdf},
-journal = {Science},
-number = {5547},
-pages = {1702--1704},
-title = {{Tree diversity in tropical rain forests: a validation of the intermediate disturbance hypothesis}},
-url = {http://www.sciencemag.org/cgi/content/full/294/5547/1702},
-volume = {294},
-year = {2001}
-}
-@article{Iwasa1995,
-abstract = {The species diversity of trees maintained in tropical rain forests is much higher than in temperate, boreal, or seasonally dry tropical forests. Many hypotheses have been proposed for higher diversity in tropical rain forests, including: (i) higher specialization of resource use, (ii) different mode of disturbance, (iii) smaller opportunity for competition on oligotrophic soil, (iv) higher productivity, (v) more active specific herbivores and pathogens, (vi) evolutionary/ecological history. In this paper we report mathematical models for tree-by-tree replacement. First the analysis of random drift model shows that the effect of gap size to species diversity is not very strong. Second we study phenological segregation model, which has the following assumptions: Basic mechanism for many species to coexist in the community is assumed given by the storage effect of lottery model, as species differ in seasonality in peak fruit production and in the subsequent period of high regeneration ability. Gaps formed during unfavorable season accumulate and become available for regeneration in the beginning of the growing season. The resulting synchronization of regeneration opportunity jeopardizes the coexistence of many similar species in seasonal environments. Analysis of a mathematical model shows: (1) the existence of unfavorable season can greatly reduce the diversity of coexisting species. (2) Diversity in the equilibrium community can be high when niche width of each species is broad and resource use is strongly overlapped. (3) Equilibrium community may include several distinct groups of species differing in phenology of regeneration. Effect of unequal niche width and frequency dependent regeneration are also examined.},
-author = {Iwasa, Y. and Kubo, T. and Sato, K.},
-doi = {10.1007/bf00044678},
-journal = {Vegetatio},
-number = {1-2},
-pages = {127--134},
-title = {{Maintenance of forest species diversity and latitudinal gradient}},
-volume = {121},
-year = {1995}
-}
-@unpublished{Duranton2002,
-abstract = {To study the detailed location patterns of industries, and particularly the tend- ency for industries to cluster relative to overall manufacturing, we develop distance-based tests of localisation. In contrast to previous studies, our approach allows us to assess the statistical significance of departures from randomness. In addition, we treat space as continuous instead of using an arbitrary collection of geographical units. This avoids problems relating to scale and borders. We apply these tests to an exhaustive UK data set. For four-digit industries, we find that (i) 52{\%} of them are localised at a 5{\%}confidence level, (ii) localisation takes place mostly at small scales below 50 kilometres, (iii) the degree of localisation is very skewed, and (iv) industries follow broad sectoral patterns with respect to localisation. Depending on the industry, smaller establishments can be the main drivers of both localisation and dispersion. Three-digit sectors show similar patterns of localisation at small scales aswell as a tendency to localise atmedium scales.},
-address = {London},
-author = {Duranton, Gilles and Overman, Henry G},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton, Overman - 2002 - Testing for Localization Using Micro-Geographic Data.pdf:pdf},
-institution = {Centre for Economic Policy Research},
-publisher = {CEPR},
-series = {CEPR Discussion Papers},
-title = {{Testing for Localization Using Micro-Geographic Data}},
-year = {2002}
-}
-@article{Vila2011,
-abstract = {Mutual information is one of the mostly used measures for evaluating image similarity. In this paper, we investigate the application of three different Tsallis-based generalizations of mutual information to analyze the similarity between scanned documents. These three generalizations derive from the Kullback–Leibler distance, the difference between entropy and conditional entropy, and the Jensen–Tsallis divergence, respectively. In addition, the ratio between these measures and the Tsallis joint entropy is analyzed. The performance of all these measures is studied for different entropic indexes in the context of document classification and registration. Keywords:},
-author = {Vila, M{\`{a}}rius and Bardera, Anton and Feixas, Miquel and Sbert, Mateu},
-doi = {10.3390/e13091694},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vila et al. - 2011 - Tsallis Mutual Information for Document Classification.pdf:pdf},
-journal = {Entropy},
-number = {12},
-pages = {1694--1707},
-title = {{Tsallis Mutual Information for Document Classification}},
-url = {http://www.mdpi.com/1099-4300/13/9/1694/},
-volume = {13},
-year = {2011}
-}
-@article{Amiti1998,
-abstract = {'New' trade theories and the 'new economic geography' theories make a number of predictions about the characteristics of the industries we should expect to become geographically concentrated and the characteristics of the countries where these locate. This paper surveys empirical studies that have evaluated these new trade theories in the light of the EU's experience. Consistent with new trade theories, empirical studies suggest that geographically concentrated industries are subject to scale economies and have a high proportion of intermediate inputs in final production; and they concentrate in countries that have access to large markets.},
-author = {Amiti, Mary},
-doi = {10.1093/oxrep/14.2.45},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Amiti - 1998 - New Trade Theories and Industrial Location in the EU A survey of evidence.pdf:pdf},
-journal = {Oxford Review of Economic Policy},
-number = {2},
-pages = {45--53},
-title = {{New Trade Theories and Industrial Location in the EU: A survey of evidence}},
-url = {https://academic.oup.com/oxrep/article/14/2/45/515163/New-trade-theories-and-industrial-location-in-the},
-volume = {14},
-year = {1998}
-}
-@article{Diaz2004,
-abstract = {Question: A set of easily-measured ('soft') plant traits has been identified as potentially useful predictors of ecosystem functioning in previous studies. Here we aimed to discover whether the screening techniques remain operational in widely contrasted circumstances, to test for the existence of axes of variation in the particular sets of traits, and to test for their links with 'harder' traits of proven importance to ecosystem functioning. Location: central-western Argentina, central England, northern upland Iran, and north-eastern Spain. Recurrent patterns of ecological specialization: Through ordination of a matrix of 640 vascular plant taxa by 12 standardized traits, we detected similar patterns of specialization in the four floras. The first PCA axis was identified as an axis of resource capture, usage and release. PCA axis 2 appeared to be a size-related axis. Individual PCA for each country showed that the same traits remained valuable as predictors of resource capture and utilization in all of them, despite their major differences in climate, biogeography and land-use. The results were not significantly driven by particular taxa: the main traits determining PCA axis 1 were very similar in eudicotyledons and monocotyledons and Asteraceae, Fabaceae and Poaceae. Links between recurrent suites of 'soft' traits and 'hard' traits: The validity of PCA axis 1 as a key predictor of resource capture and utilization was tested by comparisons between this axis and values of more rigorously established predictors ('hard' traits) for the floras of Argentina and England. PCA axis 1 was correlated with variation in relative growth rate, leaf nitrogen content, and litter decomposition rate. It also coincided with palatability to model generalist herbivores. Therefore, location on PCA axis 1 can be linked to major ecosystem processes in those habitats where the plants are dominant. Conclusion: We confirm the existence at the global scale of a major axis of evolutionary specialization, previously recognised in several local floras. This axis reflects a fundamental trade-off between rapid acquisition of resources and conservation of resources within well-protected tissues. These major trends of specialization were maintained across different environmental situations (including differences in the proximate causes of low productivity, i.e. drought or mineral nutrient deficiency). The trends were also consistent across floras and major phylogenetic groups, and were linked with traits directly relevant to ecosystem processes.},
-author = {D{\'{i}}az, Sandra and Hodgson, J. G. and Thompson, Ken and Cabido, Marcelo and Cornelissen, Johannes H. C. and Jalili, A. and Montserrat-Marti, G. and Grime, J. P. and Zarrinkamar, F. and Asri, Y. and Band, S. R. and Basconcelo, S. and Castro-Diez, P. and Funes, G. and Hamzehee, B. and Khoshnevi, M. and Perez-Harguindeguy, N. and Perez-Rontome, M. C. and Shirvany, F. A. and Vendramini, F. and Yazdani, S. and Abbas-Azimi, R. and Bogaard, A. and Boustani, S. and Charles, M. and Dehghan, M. and de Torres-Espuny, L. and Falczuk, V. and Guerrero-Campo, J. and Hynd, A. and Jones, G. and Kowsary, E. and Kazemi-Saeed, F. and Maestro-Martinez, M. and Romo-Diez, A. and Shaw, S. and Siavash, B. and Villar-Salvador, P. and Zak, M. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diaz et al. - 2004 - The plant traits that drive ecosystems Evidence from three continents.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {295--304},
-title = {{The plant traits that drive ecosystems: Evidence from three continents}},
-volume = {15},
-year = {2004}
-}
-@article{Thomas1949,
-author = {Thomas, Marjorie},
-doi = {10.2307/2332526},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thomas - 1949 - A generalization of Poisson's binomial limit for use in ecology.pdf:pdf},
-journal = {Biometrika},
-number = {1/2},
-pages = {18--25},
-title = {{A Generalization of Poisson's Binomial Limit for Use in Ecology}},
-url = {http://www.jstor.org/stable/2332526},
-volume = {36},
-year = {1949}
-}
-@article{Barlet2013,
-abstract = {We study the location patterns of business-oriented service and manufacturing industries in France. We develop a new test of localization considering space as continuous. Our test relies on a measure of divergence in the space of density distributions that allows us to assess whether or not the density distribution of bilateral distances between all pairs of plants within an industry significantly departs from randomness. We improve the test proposed by Duranton and Overman (2005), which proves to be biased with respect to the number of plants in the industry under scrutiny. Our test does not suffer from such a bias. This property is crucial for the French case where industrial concentrations of service and manufacturing industries drastically differ. With this distance-based method, we highlight some distinctive locational features of service industries that have not been mentioned in the literature so far. We show that: 1/service industries diverge more often from randomness than manufacturing industries, 2/a majority of diverging service industries are localized at very short distances (less than 4 km) whereas a majority of manufacturing industries are localized at longer distances or even dispersed, 3/within a majority of service industries, the largest plants appear localized at shorter distances than other plants, 4/within most service industries, incoming plants reduce localization whereas exiting plants reinforce it over the period 1996-2005. (C) 2012 Elsevier B.V. All rights reserved.},
-annote = {ISI Document Delivery No.: 111QZ
-Times Cited: 0
-Cited Reference Count: 32
-Barlet, M. Briant, A. Crusson, L.
-Elsevier science bv
-Amsterdam},
-author = {Barlet, M. and Briant, Anthony and Crusson, L.},
-doi = {10.1016/j.regsciurbeco.2012.08.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barlet, Briant, Crusson - 2013 - Location patterns of service industries in France A distance-based approach.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {2},
-pages = {338--351},
-title = {{Location patterns of service industries in France: A distance-based approach}},
-volume = {43},
-year = {2013}
-}
-@article{Schleuter2010,
-abstract = {Functional diversity is the diversity of species traits in ecosystems. This concept is increasingly used in ecological research, yet its formal definition and measurements are currently under discussion. As the overall behavior and consistency of functional diversity indices have not been described so far, the novice user risks choosing an inaccurate index or a set of redundant indices to represent functional diversity. In our study we closely examine functional diversity indices to clarify their accuracy, consistency, and independence. Following current theory, we categorize them into functional richness, evenness, or divergence indices. We considered existing indices as well as new indices developed in this study. The new indices aimed at remedying the weaknesses of currently used indices (e.g., by taking into account intraspecific variability). Using virtual data sets, we test (1) whether indices respond to community changes as expected from their category and (2) whether the indices within each category are consistent and independent of indices from other categories. We also test the accuracy of methods proposed for the use of categorical traits. Most classical functional richness indices either failed to describe functional richness or were correlated with functional divergence indices. We therefore recommend using the new functional richness indices that consider intraspecific variability and thus empty space in the functional niche space. In contrast, most functional evenness and divergence indices performed well with respect to all proposed tests. For categorical variables, we do not recommend blending discrete and real-valued traits (except for indices based on distance measures) since functional evenness and divergence have no transposable meaning for discrete traits. Nonetheless, species diversity indices can be applied to categorical traits (using trait levels instead of species) in order to describe functional richness and equitability},
-author = {Schleuter, Diana and Daufresne, M. and Massol, F. and Argillier, Christine},
-doi = {10.1890/08-2225.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schleuter et al. - 2010 - A user's guide to functional diversity indices.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {469--484},
-title = {{A user's guide to functional diversity indices}},
-url = {http://www.esajournals.org/doi/abs/10.1890/08-2225.1},
-volume = {80},
-year = {2010}
-}
-@book{Overman2001,
-abstract = {This paper surveys the empirical literature on the economic geography of trade flows, factor prices, and the location of production. The discussion is structured around the empirical predictions of a canonical theoretical model. We review empirical evidence on the determinants of trade costs and the effects of these costs on trade flows. Geography is a major determinant of factor prices, and access to foreign markets alone is shown to explain some 35{\%} of the cross-country variation in per capita income. The paper documents empirical findings of home market (or magnification) effects, suggesting that imperfectly competitive industries are drawn more than proportionately to locations with good market access. Sub-national evidence establishes the presence of industrial clustering, and we examine the roles played by product market linkages to customer and supplier firms, knowledge spillovers, and labour market externalities.},
-author = {Overman, Henry G. and Redding, Stephen J. and Venables, Anthony J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Overman, Redding, Venables - 2001 - The Economic Geography of Trade, Production, and Income A Survey of Empirics.pdf:pdf},
-publisher = {Centre for Economic Performance},
-title = {{The Economic Geography of Trade, Production, and Income: A Survey of Empirics}},
-url = {http://cep.lse.ac.uk/pubs/download/dp0508.pdf},
-year = {2001}
-}
-@book{Sokal1963,
-abstract = {Numerical taxonomy is defined in this book, the first to deal comprehensively with the subject, as " the numerical evaluation of the affinity or similarity between taxonomic units and the ordering of these units into taxa on the basis of their affinities ", and its outstanding aims are stated to be repeatability and objectivity. The book has ten chapters. The first is introductory, and the second is a critique of conventional taxonomic methods. The third deals with new methods, including numerical methods, comparative serology and polyphenic methods (those yielding many characters in a single technical procedure) such as chromatography, electrophoresis and infra-red spectroscopy. The fourth is an exposition of the aims and principles of numerical taxonomy. In this, the comparison is based on as many characters as possible, every character being given equal weight and over-all similarity of two entities being a function of the similarity of the many characters compared. Distinct taxa are constructed on the basis of diverse character correlations in the groups under study. The process is empirical and is independent of phylogenetic considerations. The fifth chapter is a discussion of the choice of characters, their coding for mathematical manipulation and the selection of organisms for study, and the sixth and seventh deal with the estimation of taxonomic resemblance between organisms and the grouping of organisms into taxa on the basis of these resemblances. The eighth and ninth comprise discussions of the relation of numerical taxonomy to phytogeny and palaeontology and to nomenclature and diagnostic keys. The last refers to future developments and similar work in subjects other than the classification of living creatures. Details of the mathematical methods of numerical taxonomy, illustrated by elementary examples, are given in an appendix.},
-address = {San Francisco},
-author = {Sokal, Robert R. and Sneath, P. H. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Sokal, Sneath - 1963 - Principles of numerical taxonomy.pdf:pdf},
-publisher = {W. H. Freeman {\&} Co.},
-title = {{Principles of numerical taxonomy}},
-year = {1963}
-}
-@article{Goreaud1999,
-abstract = {The analysis of spatial pattern in plant ecology usually implies to solve some edge effect problems. We present in this paper some explicit formulas of edge effect correction that should enable plant ecologists to analyse a wider range of real field data. We consider the local correcting factor of edge effect for Ripley's K-function, that can also be used for other statistics of spatial analysis based on the counting of neighbours within a given distance. For both circular and rectangular study areas, we provide a review of explicit formulas and an extension of these formulas for long and narrow plots. In the case of irregular-shaped study areas, we propose a generalisation of the method that computes edge effect correction by excluding triangular surfaces from a simple (rectangular or circular) initial shape. A short example in forest ecology, where the soil characteristics determine a study plot of complex shape, illustrate how this edge effect correction can be efficient to avoid misinterpretations.},
-author = {Goreaud, Fran{\c{c}}ois and P{\'{e}}lissier, Rapha{\"{e}}l},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {433--438},
-title = {{On explicit formulas of edge-effect correction for Ripley's K-function}},
-volume = {10},
-year = {1999}
-}
-@techreport{Barthes1991a,
-address = {Cayenne},
-author = {Barthes, Bernard},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barthes - 1991 - Caract{\'{e}}risation p{\'{e}}dologique de parcelles du dispositif For{\^{e}}t Naturelle du C.T.F.T. {\`{a}} Paracou (Sinnamary, Guyane).pdf:pdf},
-pages = {14 p},
-publisher = {ORSTOM},
-title = {{Caract{\'{e}}risation p{\'{e}}dologique de parcelles du dispositif "For{\^{e}}t Naturelle" du C.T.F.T. {\`{a}} Paracou (Sinnamary, Guyane)}},
-year = {1991}
-}
-@article{Beguinot2016,
-abstract = {A lot of nonparametric estimators of the number of unrecorded species after partial sampling of an assemblage of species, have been proposed in the literature. Unfortunately, these different types of estimators provides substantially divergent predictions. While empirical comparisons have failed to consistently select in favour of one among all these estimators, a new approach, based on more theoretical ground, has proven that among three of the most commonly used nonparametric estimators, Chao, Jackknife-1 and Jackknife-2, the latter was the best choice in most cases while Chao or Jackknife-1 should preferably be restricted to samplings approaching completeness. Here, I propose an alternative approach, aiming also at discriminating between the same three estimators on the basis of another theoretical argument: The necessary compliance with the required “rule of additivity”, according to which, if an assemblage of species is made of several, distinct groups of species, the estimation of species richness for the whole assemblage should be exactly the sum of the estimations of richness for each group of species. Referring to this rule of additivity, the Jackknife series of estimators (and in particular Jackknife-2 when samples remain far from completeness), proves, once again, being satisfactory in full generality. This strengthens the estimators of the Jackknife series as being particularly appropriate to evaluate, in most cases, the number of unrecorded species of a partially sampled assemblage and the corresponding total species richness of the assemblage.},
-author = {B{\'{e}}guinot, Jean},
-doi = {10.9734/ARRB/2016/25104},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/B{\'{e}}guinot - 2016 - Basic Theoretical Arguments Advocating Jackknife-2 as Usually being the Most Appropriate Nonparametric Estimator of To.pdf:pdf},
-journal = {Annual Research {\&} Review in Biology},
-number = {1},
-pages = {1--12},
-title = {{Basic Theoretical Arguments Advocating Jackknife-2 as Usually being the Most Appropriate Nonparametric Estimator of Total Species Richness}},
-url = {http://sciencedomain.org/abstract/13904},
-volume = {10},
-year = {2016}
-}
-@article{Ribeiro2003,
-abstract = {In this work, we investigated the spatial distribution of two sessile insect herbivores over the entire range of their host plant, Coccoloba cereifera, a sclerophyllous shrub endemic to Serra do Cipo, Brazil. The two insects have very distinct life histories and dispersal behaviours and we hypothesized that their classification into behavioural syndromes could be used to predict their spatial distribution patterns. Abgrallaspis cyanophylli (Homoptera) is an armoured scale insect that fits well into the eruptive syndrome. Stenapion aff. contrarium (Coleoptera) is a petiole borer with wide search capabilities, which fits into the latent syndrome. We expected that Abgrallaspis would follow the host plant aggregation pattern whereas Stenapion would be distributed more uniformly through the region and be less affected by host aggregation. We counted the number of attacked and non-attacked ramets within two perpendicular belt transects as well as within a 20 m x 20 m quadrat placed over a dense shrub aggregation. Local quadrat covariance methods were used to estimate the spatial pattern of each insect. At fine scales, we found Stenapion evenly distributed over the host plant and Abgrallaspis with a significantly aggregated pattern. This finding is in accordance with our hypothesis. At larger scales, however, this pattern was lost and the results were largely variable. We conclude that the classification of insects into behavioural syndromes may be useful to predict distribution patterns at fine scales. At larger scales, however, history and chance events may be more important.},
-annote = {Article
-English
-AUSTRAL ECOL
-665HH},
-author = {Ribeiro, K. T. and Codeco, C. T. and Fernandes, G. W.},
-doi = {10.1046/j.1442-9993.2003.01235.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ribeiro, Codeco, Fernandes - 2003 - Local and regional spatial distribution of an eruptive and a latent herbivore insect species.pdf:pdf},
-journal = {Austral Ecology},
-number = {2},
-pages = {99--107},
-title = {{Local and regional spatial distribution of an eruptive and a latent herbivore insect species}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1442-9993.2003.01235.x/abstract},
-volume = {28},
-year = {2003}
-}
-@article{Campbell1985,
-author = {Campbell, L. L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Campbell - 1985 - The relation between information theory and the differential geometry approach to statistics.pdf:pdf},
-journal = {Information sciences},
-number = {3},
-pages = {199--210},
-title = {{The relation between information theory and the differential geometry approach to statistics}},
-url = {http://www.sciencedirect.com/science/article/pii/0020025585900507},
-volume = {35},
-year = {1985}
-}
-@article{Wright2006a,
-abstract = {Light availability generally decreases vertically downwards through plant canopies. According to optimisation theory, in order to maximise canopy photosynthesis plants should allocate leaf nitrogen per area (N-area) in parallel with vertical light gradients, and leaf mass per area (LMA) and leaf angles should decrease down through the canopy also. Many species show trends consistent with these predictions, although these are never as steep as predicted. Most studies of canopy gradients in leaf traits have concerned tall herbaceous vegetation or forest trees. But do evergreen species from open habitats also show these patterns? We quantified gradients of light availability, LMA, leaf N and phosphorus ( P), and leaf angle along leaf age sequences and vertical canopy profiles, across 28 woody species from open habitats in eastern Australia. The observed trends in LMA, Narea and leaf angle largely conflicted with expectations from canopy optimisation models, whereas trends in leaf P were more consistent with optimal allocation. These discrepancies most likely relate to these species having rather open canopies with quite shallow light gradients, but also suggest that modelling the co-optimisation of resources other than nitrogen is required for understanding plant canopies.},
-author = {Wright, Ian J. and Leishman, Michelle R. and Read, C. and Westoby, Mark},
-doi = {10.1071/FP05319},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2006 - Gradients of light availability and leaf traits with leaf age and canopy position in 28 Australian shrubs and tre.pdf:pdf},
-journal = {Functional Plant Biology},
-number = {5},
-pages = {407--419},
-title = {{Gradients of light availability and leaf traits with leaf age and canopy position in 28 Australian shrubs and trees}},
-url = {http://www.publish.csiro.au/fp/FP05319},
-volume = {33},
-year = {2006}
-}
-@article{Munoz2013,
-abstract = {Neutral community models have shown that limited migration can have a pervasive influence on the taxonomic composition of local communities even when all individuals are assumed of equivalent ecological fitness. Notably, the spatially implicit neutral theory yields a single parameter / for the immigration-drift equilibrium in a local community. In the case of plants, seed dispersal is considered as a defining moment of the immigration process and has attracted empirical and theoretical work. In this paper, we consider a version of the immigration parameter / depending on dispersal limitation from the neighbourhood of a community. Seed dispersal distance is alternatively modelled using a distribution that decreases quickly in the tails (thin-tailed Gaussian kernel) and another that enhances the chance of dispersal events over very long distances (heavily fat-tailed Cauchy kernel). Our analysis highlights two contrasting situations, where / is either mainly sensitive to community size (related to ecological drift) under the heavily fat-tailed kernel or mainly sensitive to dispersal distance under the thin-tailed kernel. We review dispersal distances of rainforest trees from field studies and assess the consistency between published estimates of / based on spatially-implicit models and the predictions of the kernel-based model in tropical forest plots. Most estimates of / were derived from large plots (10-50 ha) and were too large to be accounted for by a Cauchy kernel. Conversely, a fraction of the estimates based on multiple smaller plots (1 ha) appeared too small to be consistent with reported ranges of dispersal distances in tropical forests. Very large estimates may reflect within-plot habitat heterogeneity or estimation problems, while the smallest estimates likely imply other factors inhibiting migration beyond dispersal limitation. Our study underscores the need for interpreting / as an integrative index of migration limitation which, besides the limited seed dispersal, possibly includes habitat filtering or fragmentation.},
-author = {Munoz, Fran{\c{c}}ois and Beeravolu, Champak R. and P{\'{e}}lissier, Rapha{\"{e}}l and Couteron, Pierre},
-doi = {10.1371/journal.pone.0072497},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Munoz et al. - 2013 - Do Spatially-Implicit Estimates of Neutral Migration Comply with Seed Dispersal Data in Tropical Forests.PDF:PDF},
-journal = {Plos One},
-number = {8},
-title = {{Do Spatially-Implicit Estimates of Neutral Migration Comply with Seed Dispersal Data in Tropical Forests?}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072497},
-volume = {8},
-year = {2013}
-}
-@book{Mayr1970,
-address = {Cambridge, Massachussets},
-author = {Mayr, Ernst},
-isbn = {0674690109},
-publisher = {Belknap Press of Harvard University Press},
-title = {{Populations, species, and evolution}},
-year = {1970}
-}
-@article{Ricotta2007,
-abstract = {Community diversity has been studied extensively in relation to its effects on ecosystem functioning. Testing the consequences of diversity on ecosystem processes will require measures to be available based on a rigorous conceptualization of their very meaning. In the last decades, literally dozens of measures of diversity have been proposed. However, rather than using unrelated metrics, we need to identify their separate components so that possible links between them and ecosystem functioning can be examined using an agreed-upon language. In this paper, first, a short overview on new and old measures of community diversity is presented. Next, I propose a general framework in which most of the existing measures of diversity are sorted into four interrelated semantic classes: richness, abundance-weighted diversity, evenness and divergence. In this view, this paper constitutes an attempt to organize the very large number of existing diversity measures avoiding ambiguities in the meaning of the different facets of community diversity. {\^{A}}{\textcopyright} 2007 Springer Science+Business Media, B.V.},
-annote = {Cited By (since 1996): 11
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: ABIOA
-doi: 10.1007/s10441-007-9008-7
-PubMed ID: 17486413
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, Rome 00185, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1007/s10441-007-9008-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2007 - A semantic taxonomy for diversity measures.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {1},
-pages = {23--33},
-title = {{A semantic taxonomy for diversity measures}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34447527103{\&}partnerID=40{\&}md5=9b013b923dd1aecfe52f53c5611eb7a5},
-volume = {55},
-year = {2007}
-}
-@article{Bickenbach2008,
-abstract = {This article extends the methodological toolbox of measures of regional concentration of industries and industrial specialization of regions. It first defines disproportionality measures of concentration and specialization and proposes a taxonomy of these measures. This taxonomy is based on three characteristic features of any disproportionality measure. It helps researchers define the measure that fits their research purpose and data best. The article then generalizes this taxonomy to cover disproportionality measures of economic localization that evaluate specialization and concentration simultaneously and spatial disproportionality measures that deal with the checkerboard problem and the modifiable areal unit problem.},
-author = {Bickenbach, Frank and Bode, Eckhardt},
-doi = {10.1177/0160017608319589},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bickenbach, Bode - 2008 - Disproportionality Measures of Concentration, Specialization, and Localization.pdf:pdf},
-journal = {International Regional Science Review},
-number = {4},
-pages = {359--388},
-title = {{Disproportionality Measures of Concentration, Specialization, and Localization}},
-url = {http://irx.sagepub.com/content/31/4/359.abstract},
-volume = {31},
-year = {2008}
-}
-@article{Leitao2015,
-abstract = {* Spatial patterns of community composition turnover (beta diversity) may be mapped through generalised dissimilarity modelling (GDM). While remote sensing data are adequate to describe these patterns, the often high-dimensional nature of these data poses some analytical challenges, potentially resulting in loss of generality. This may hinder the use of such data for mapping and monitoring beta-diversity patterns. * This study presents Sparse Generalised Dissimilarity Modelling (SGDM), a methodological framework designed to improve the use of high-dimensional data to predict community turnover with GDM. SGDM consists of a two-stage approach, by first transforming the environmental data with a sparse canonical correlation analysis (SCCA), aimed at dealing with high-dimensional data sets, and secondly fitting the transformed data with GDM. The SCCA penalisation parameters are chosen according to a grid search procedure in order to optimise the predictive performance of a GDM fit on the resulting components. The proposed method was illustrated on a case study with a clear environmental gradient of shrub encroachment following cropland abandonment, and subsequent turnover in the bird communities. Bird community data, collected on 115 plots located along the described gradient, were used to fit composition dissimilarity as a function of several remote sensing data sets, including a time series of Landsat data as well as simulated EnMAP hyperspectral data. * The proposed approach always outperformed GDM models when fit on high-dimensional data sets. Its usage on low-dimensional data was not consistently advantageous. Models using high-dimensional data, on the other hand, always outperformed those using low-dimensional data, such as single-date multispectral imagery. * This approach improved the direct use of high-dimensional remote sensing data, such as time-series or hyperspectral imagery, for community dissimilarity modelling, resulting in better performing models. The good performance of models using high-dimensional data sets further highlights the relevance of dense time series and data coming from new and forthcoming satellite sensors for ecological applications such as mapping species beta diversity.},
-author = {Leit{\~{a}}o, Pedro J. and Schwieder, Marcel and Suess, Stefan and Catry, In{\^{e}}s and Milton, Edward J. and Moreira, Francisco and Osborne, Patrick E. and Pinto, Manuel J. and van der Linden, Sebastian and Hostert, Patrick},
-doi = {10.1111/2041-210X.12378},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leit{\~{a}}o et al. - 2015 - Mapping beta diversity from space Sparse Generalised Dissimilarity Modelling (SGDM) for analysing high-dimensiona.pdf:pdf},
-isbn = {2041-210X},
-issn = {2041210X},
-journal = {Methods in Ecology and Evolution},
-number = {7},
-pages = {764--771},
-title = {{Mapping beta diversity from space: Sparse Generalised Dissimilarity Modelling (SGDM) for analysing high-dimensional data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12378/abstract},
-volume = {6},
-year = {2015}
-}
-@article{Ihaka1996,
-abstract = {In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing computer languages. We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping.},
-author = {Ihaka, Ross and Gentleman, Robert},
-doi = {10.1080/10618600.1996.10474713},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ihaka, Gentleman - 1996 - R a language for data analysis and graphics.pdf:pdf},
-journal = {Journal of Computational and Graphical Statistics},
-number = {3},
-pages = {299--314},
-title = {{R: a language for data analysis and graphics}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/10618600.1996.10474713},
-volume = {5},
-year = {1996}
-}
-@article{Blomberg2003,
-abstract = {The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal $\alpha$ = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92{\%} of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25{\%} of traits) and/or ACDC (40{\%}) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.},
-author = {Blomberg, Simon P. and Garland, Theodore and Ives, Anthony R. and Crespi, B.},
-doi = {10.1554/0014-3820(2003)057[0717:tfpsic]2.0.co;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blomberg et al. - 2003 - Testing for phylogenetic signal in comparative data behavioral traits are more labile.pdf:pdf},
-journal = {Evolution},
-number = {4},
-pages = {717--745},
-title = {{Testing for phylogenetic signal in comparative data: behavioral traits are more labile}},
-url = {http://dx.doi.org/10.1554/0014-3820(2003)057[0717:TFPSIC]2.0.CO;2},
-volume = {57},
-year = {2003}
-}
-@article{Whittaker1952,
-author = {Whittaker, R. H.},
-doi = {10.2307/1948527},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker - 1952 - A study of summer foliage insect communities in the Great Smoky Mountains.pdf:pdf},
-journal = {Ecological monographs},
-number = {1},
-pages = {1--44},
-title = {{A study of summer foliage insect communities in the Great Smoky Mountains}},
-url = {http://www.jstor.org/stable/1948527},
-volume = {22},
-year = {1952}
-}
-@incollection{Cremer2004,
-address = {Amsterdam},
-author = {Cremer, Helmuth and Pestieau, Pierre},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-publisher = {Elsevier. North Holland},
-title = {{Factor mobility and redistribution: a survey}},
-year = {2004}
-}
-@article{Merigot2011,
-author = {M{\'{e}}rigot, Bastien and Gaertner, Jean-Claude},
-doi = {10.1002/bies.201100103},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/M{\'{e}}rigot, Gaertner - 2011 - Incorporation of phylogeny in biological diversity measurement Drawbacks of extensively used indices, and adv.pdf:pdf},
-journal = {BioEssays},
-number = {11},
-pages = {819--822},
-title = {{Incorporation of phylogeny in biological diversity measurement: Drawbacks of extensively used indices, and advantages of quadratic entropy}},
-url = {http://dx.doi.org/10.1002/bies.201100103},
-volume = {33},
-year = {2011}
-}
-@article{Pavoine2013,
-abstract = {We developed an approach for analysing the effects of two crossed factors A and B on the functional, taxonomic or phylogenetic composition of communities. The methodology, known as crossed-DPCoA, defines a space where species, communities and the levels of the two factors are organised as a set of points. In this space, the Euclidean distance between two species-specific points is a measure of the (functional, taxonomic or phylogenetic) dissimilarity. The communities are positioned at the centroid of their constitutive species; and the levels of two factors at the centroid of the communities associated with them. We develop two versions for crossed-DPCoA, the first one moves the levels of factor B to the centre of the space and analyses the axes of highest variance in the coordinates of the levels of factor A. It is related to previous ordination approaches such as partial canonical correspondence analysis and partial non-symmetrical correspondence analysis. The second version projects all points on the orthogonal complement of the space generated by the principal axes of factor B. This second version should be preferred when there is an a priori suspicion that factor A and B are associated. We apply the two versions of crossed-DPCoA to analyse the phylogenetic composition of Central European and Mediterranean bird communities. Applying crossed-DPCoA on bird communities supports the hypothesis that allopatric speciation processes during the Quaternary occurred in open and patchily distributed landscapes, while the lack of geographic barriers to dispersal among forest habitats may explain the homogeneity of forest bird communities over the whole western Palaearctic. Generalizing several ordination analyses commonly used in ecology, crossed-DPCoA provides an approach for analysing the effects of crossed factors on functional, taxonomic and phylogenetic diversity, environmental and geographic structure of species niches, and more broadly the role of genetics on population structures.},
-author = {Pavoine, Sandrine and Blondel, Jacques and Dufour, Anne-B{\'{e}}atrice and Gasc, Amandine and Bonsall, Michael B.},
-doi = {10.1371/journal.pone.0054530},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2013 - A New Technique for Analysing Interacting Factors Affecting Biodiversity Patterns Crossed-DPCoA.pdf:pdf},
-journal = {Plos One},
-number = {1},
-pages = {e54530},
-title = {{A New Technique for Analysing Interacting Factors Affecting Biodiversity Patterns: Crossed-DPCoA}},
-url = {http://dx.doi.org/10.1371{\%}2Fjournal.pone.0054530},
-volume = {8},
-year = {2013}
-}
-@article{Coste2010b,
-abstract = {Chlorophyll meters such as the SPAD-502 offer a simple, inexpensive and rapid method to estimate foliar chlorophyll content. However, values provided by SPAD-502 are unitless and require empirical calibrations between SPAD units and extracted chlorophyll values. Leaves of 13 tree species from the tropical rain forest in French Guiana were sampled to select the most appropriate calibration model among the often-used linear, polynomial and exponential models, in addition to a novel homographic model that has a natural asymptote. The homographic model best accurately predicted total chlorophyll content (mu g cm(-2)) from SPAD units (R-2 = 0.89). Interspecific differences in the homographic model parameters explain less than 7{\%} of the variation in chlorophyll content in our data set. The utility of the general homographic model for a variety of research and management applications clearly outweighs the slight loss of model accuracy due to the abandon of the species' effect.},
-annote = {From Duplicate 2 ( Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter: a calibration test with thirteen tree species of tropical rainforest in French Guiana - Coste, Sabrina; Baraloto, Christopher; Leroy, C{\'{e}}line; Marcon, {\'{E}}ric; Renaud, Am{\'{e}}lie; Richardson, Andrew D; Roggy, Jean-Christophe; Schimann, Heidy; Uddling, Johan; H{\'{e}}rault, Bruno )
-
-ISI Document Delivery No.: 656QA
-Times Cited: 0
-Cited Reference Count: 20
-Coste, Sabrina Baraloto, Christopher Leroy, Celine Marcon, Eric Renaud, Amelie Richardson, Andrew D. Roggy, Jean-Christophe Schimann, Heidy Uddling, Johan Herault, Bruno
-EDP SCIENCES S A
-LES ULIS CEDEX A},
-author = {Coste, Sabrina and Baraloto, Christopher and Leroy, C{\'{e}}line and Marcon, Eric and Renaud, Am{\'{e}}lie and Richardson, Andrew D. and Roggy, Jean-Christophe and Schimann, Heidy and Uddling, Johan and H{\'{e}}rault, Bruno},
-doi = {10.1051/forest/2010020},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coste et al. - 2010 - Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter a calibration test with thirteen tree sp.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {6},
-pages = {607},
-title = {{Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter: a calibration test with thirteen tree species of tropical rainforest in French Guiana}},
-url = {http://link.springer.com/10.1051/forest/2010020},
-volume = {67},
-year = {2010}
-}
-@article{Loreau2013,
-abstract = {There is mounting evidence that biodiversity increases the stability of ecosystem processes in changing environments, but the mechanisms that underlie this effect are still controversial and poorly understood. Here, we extend mechanistic theory of ecosystem stability in competitive communities to clarify the mechanisms underlying diversity-stability relationships. We first explain why, contrary to a widely held belief, interspecific competition should generally play a destabilising role. We then explore the stabilising effect of differences in species' intrinsic rates of natural increase and provide a synthesis of various potentially stabilising mechanisms. Three main mechanisms are likely to operate in the stabilising effects of biodiversity on ecosystem properties: (1) asynchrony of species' intrinsic responses to environmental fluctuations, (2) differences in the speed at which species respond to perturbations, (3) reduction in the strength of competition. The first two mechanisms involve temporal complementarity between species, while the third results from functional complementarity. Additional potential mechanisms include selection effects, behavioural changes resulting from species interactions and mechanisms arising from trophic or non-trophic interactions and spatial heterogeneity. We conclude that mechanistic trait-based approaches are key to predicting the effects of diversity on ecosystem stability and to bringing the old diversity-stability debate to a final resolution.},
-author = {Loreau, Michel and de Mazancourt, Claire},
-doi = {10.1111/ele.12073},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau, de Mazancourt - 2013 - Biodiversity and ecosystem stability A synthesis of underlying mechanisms.pdf:pdf},
-isbn = {1461-0248},
-issn = {1461023X},
-journal = {Ecology Letters},
-number = {Suppl.1},
-pages = {106--115},
-title = {{Biodiversity and ecosystem stability: A synthesis of underlying mechanisms}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12073/abstract},
-volume = {16},
-year = {2013}
-}
-@article{Ricotta2011,
-abstract = {Assessing the effects of environmental constraints on community structure often relies on methods that consider changes in species functional traits in response to environmental processes. Various indices have been proposed to measure relevant aspects of community trait composition from different viewpoints and perspectives. Among these, the 'community-weighted mean trait value' (CWM) and the Rao coefficient have been widely used in ecological research for summarizing different facets of functional composition and diversity. Analyzing changes in functional diversity of bee communities along a post-fire successional gradient in southern Switzerland we show that these two measures may be used to describe two complementary aspects of community structure, such as the mean and the dispersion of functional traits within a given species assemblage. While CWM can be adequately used to summarize shifts in mean trait values within communities due to environmental selection for certain functional traits, the Rao coefficient can be effectively applied to analyze patterns of trait convergence or divergence compared to a random expectation.},
-author = {Ricotta, Carlo and Moretti, Marco},
-doi = {10.1007/s00442-011-1965-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Moretti - 2011 - CWM and Rao's quadratic diversity A unified framework for functional ecology.pdf:pdf},
-journal = {Oecologia},
-pages = {181--188},
-title = {{CWM and Rao's quadratic diversity: A unified framework for functional ecology}},
-volume = {167},
-year = {2011}
-}
-@article{Liang2016,
-abstract = {The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries andmost terrestrial biomes,we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivityworldwide.The value of biodiversity inmaintaining commercial forest productivity alone—US{\$}166 billion to 490 billion per year according to our estimation—ismore than twice what it would cost to implement effective global conservation.This highlights the need for a worldwide reassessment of biodiversity values, forestmanagement strategies, and conservation priorities.},
-author = {Liang, Jingjing and Crowther, Thomas W. and Picard, Nicolas and Wiser, Susan and Zhou, Mo and Alberti, Giorgio and Schulze, Ernst-Detlef and McGuire, David and Bozzato, Fabio and Pretzsch, Hans and De-Miguel, Sergio and Paquette, Alain and H{\'{e}}rault, Bruno and Scherer-Lorenzen, Michael and Barrett, Christopher B. and Glick, Henry B. and Hengeveld, Geerten M. and Nabuurs, Gert-Jan and Pfautsch, Sebastian and Viana, Helder and Vibrans, Alexander C. and Ammer, Christian and Schall, Peter and Verbyla, David and Tchebakova, Nadja and Fischer, Markus and Watson, James V. and Chen, Han Y. H. and Lei, Xiangdong and Schelhaas, Mart-Jan and Lu, Huicui and Gianelle, Damiano and Parfenova, Elena I. and Salas, Christian and Lee, Eungul and Lee, Boknam and Kim, Hyun Seok and Bruelheide, Helge and Coomes, David A. and Piotto, Daniel and Sunderland, Terry and Schmid, Bernhard and Gourlet-Fleury, Sylvie and Sonk{\'{e}}, Bonaventure and Tavani, Rebecca and Zhu, Jun and Brandl, Susanne and Vayreda, Jordi and Kitahara, Fumiaki and Searle, Eric B. and Neldner, Victor J. and Ngugi, Michael R. and Baraloto, Christopher and Frizzera, Lorenzo and Ba{\l}azy, Radomir and Oleksyn, Jacek and Zawi{\l}a-Nied{\'{z}}wiecki, Tomasz and Bouriaud, Olivier and Bussotti, Filippo and Fin{\'{e}}r, Leena and Jaroszewicz, Bogdan and Jucker, Tommaso and Valladares, Fernando and Jagodzinski, Andrzej M. and Peri, Pablo L. and Gonmadje, Christelle and Marthy, William and O'Brien, Timothy and Martin, Emanuel H. and Marshall, Andy and Rovero, Francesco and Bitariho, Robert and Niklaus, Pascal A. and Alvarez-Loayza, Patricia and Chamuya, Nurdin and Valencia, Renato and Mortier, Fr{\'{e}}d{\'{e}}ric and Wortel, Verginia and Engone-Obiang, Nestor L. and Ferreira, Leandro V. and Odeke, David E. and Vasquez, Rodolfo M. and Reich, Peter B.},
-doi = {10.1126/science.aaf8957},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liang et al. - 2016 - Positive biodiversity–productivity relationship predominant in global forests.pdf:pdf},
-journal = {Science},
-number = {6309},
-pages = {196},
-title = {{Positive biodiversity–productivity relationship predominant in global forests}},
-url = {http://science.sciencemag.org/content/354/6309/aaf8957},
-volume = {354},
-year = {2016}
-}
-@misc{Fortunel2016a,
-abstract = {Understanding the mechanisms generating species distributions remains a challenge, especially in hyperdiverse tropical forests. We evaluated the role of rainfall variation, soil gradients and herbivory on seedling mortality, and how variation in seedling performance along these gradients contributes to habitat specialisation. In a 4-year experiment, replicated at the two extremes of the Amazon basin, we reciprocally transplanted 4638 tree seedlings of 41 habitat-specialist species from seven phylogenetic lineages among the three most important forest habitats of lowland Amazonia. Rainfall variation, flooding and soil gradients strongly influenced seedling mortality, whereas herbivory had negligible impact. Seedling mortality varied strongly among habitats, consistent with predictions for habitat specialists in most lineages. This suggests that seedling performance is a primary determinant of the habitat associations of adult trees across Amazonia. It further suggests that tree diversity, currently mostly harboured in terra firme forests, may be strongly impacted by the predicted climate changes in Amazonia.},
-author = {Fortunel, Claire and Paine, C. E.Timothy and Fine, Paul V.A. and Mesones, Italo and Goret, Jean Yves and Burban, Benoit and Cazal, Jocelyn and Baraloto, Christopher},
-booktitle = {Ecology letters},
-doi = {10.1111/ele.12661},
-number = {10},
-pages = {1256--1266},
-title = {{There's no place like home: seedling mortality contributes to the habitat specialisation of tree species across Amazonia}},
-volume = {19},
-year = {2016}
-}
-@article{Carroll2008,
-abstract = {Most cluster-based economic development programs use co-location to initially identify the spatial footprint of cluster areas. Geographic proximity (co- location) is a necessary, but not a sufficient, condition for potential clustering activity. Therefore, an assessment of industry location and density patterns becomes the first phase in the identification of potential cluster regions to be included in a cluster driven development policy. This paper compares the use of location quotients and Getis–Ord G i * in the identification of potential cluster regions in the transportation equipment industry of four states in the Midwestern USA. Also, both location quotients and G i * are used to classify counties with respect to their concentration of transportation equipment manufacturing.},
-author = {Carroll, Michael and Reid, Neil and Smith, Bruce},
-doi = {10.1007/s00168-007-0163-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carroll, Reid, Smith - 2008 - Location quotients versus spatial autocorrelation in identifying potential cluster regions.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {2},
-pages = {449--463},
-title = {{Location quotients versus spatial autocorrelation in identifying potential cluster regions}},
-url = {http://dx.doi.org/10.1007/s00168-007-0163-1},
-volume = {42},
-year = {2008}
-}
-@article{Torgerson1952,
-abstract = {Multidimensional scaling can be considered as involving three basic steps. In the first step, a scale of comparative distances between all pairs of stimuli is obtained. This scale is analogous to the scale of stimuli obtained in the traditional paired comparisons methods. In this scale, however, instead of locating each stimulus-object on a given continuum, the distances between each pair of stimuli are located on a distance continuum. As in paired comparisons, the procedures for obtaining a scale of comparative distances leave the true zero point undetermined. Hence, a comparative distance is not a distance in the usual sense of the term, but is a distance minus an unknown constant. The second step involves estimating this unknown constant. When the unknown constant is obtained, the comparative distances can be converted into absolute distances. In the third step, the dimensionality of the psychological space necessary to account for these absolute distances is determined, and the projections of stimuli on axes of this space are obtained. A set of analytical procedures was developed for each of the three steps given above, including a least-squares solution for obtaining comparative distances by the complete method of triads, two practical methods for estimating the additive constant, and an extension of Young and Householder's Euclidean model to include procedures for obtaining the projections of stimuli on axes from fallible absolute distances.},
-author = {Torgerson, Warren S},
-doi = {10.1007/BF02288916},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Torgerson - 1952 - Multidimensional scaling I. Theory and method.pdf:pdf},
-journal = {Psychometrica},
-number = {4},
-pages = {401--419},
-title = {{Multidimensional scaling: I. Theory and method}},
-volume = {17},
-year = {1952}
-}
-@article{Kosman2007,
-abstract = {Measures of diversity within populations, and distance between populations, are compared for organisms with an asexual or mixed mode of reproduction. Examples are drawn from studies of plant pathogenic fungi based on binary traits including presence/absence of DNA bands or virulence/avirulence to differential hosts. Commonly used measures of population diversity or genetic distance consider either genotype frequencies or allele frequencies. Kosman's diversity and distance measures are the most suitable for populations with an asexual or mixed mode of reproduction, because by considering genetic patterns of all individuals they take into account not just the genotype frequencies but also the genetic similarities between genotypes in the populations. The Kosman distance and diversity measures for populations can be calculated using different measures of dissimilarity between individuals (the simple mismatch, Jaccard and Dice coefficients of dissimilarity). Kosman's distances based on the simple mismatch and Jaccard dissimilarities are metrics. Comparisons of diversity indices for hypothetical examples as well as for actual data sets are presented to demonstrate that inferences from diversity analysis of populations can be driven by techniques of diversity and distance assessments and not only data driven.},
-author = {Kosman, Evsey and Leonard, Kurt J},
-doi = {10.1111/j.1469-8137.2007.02031.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosman, Leonard - 2007 - Conceptual analysis of methods applied to assessment of diversity within and distance between populations with.pdf:pdf},
-journal = {The New phytologist},
-number = {3},
-pages = {683--96},
-title = {{Conceptual analysis of methods applied to assessment of diversity within and distance between populations with asexual or mixed mode of reproduction.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/17447922},
-volume = {174},
-year = {2007}
-}
-@article{Peres-Neto2003,
-abstract = {Principal component analysis (PCA) is one of the most commonly used tools in the analysis of ecological data. This method reduces the effective dimensionality of a multivariate data set by producing linear combinations of the original variables (i.e., components) that summarize the predominant patterns in the data. In order to provide meaningful interpretations for principal components, it is important to determine which variables are associated with particular components. Some data analysts incorrectly test the statistical significance of the correlation between original variables and multivariate scores using standard statistical tables. Others interpret eigenvector coefficients larger than an arbitrary absolute value (e.g., 0.50). Resampling, randomization techniques, and parallel analysis have been applied in a few cases. In this study, we compared the performance of a variety of approaches for assessing the significance of eigenvector coefficients in terms of type I error rates and power. Two novel approaches based on the broken-stick model were also evaluated. We used a variety of simulated scenarios to examine the influence of the number of real dimensions in the data; unique versus complex variables the magnitude of eigenvector coefficients; and the number of variables associated with a particular dimension. Our results revealed that bootstrap confidence intervals and a modified bootstrap confidence interval for the broken-stick model proved to be the most reliable techniques.},
-author = {Peres-Neto, Pedro R. and Jackson, Donald A. and Somers, Keith M.},
-doi = {10.1890/00-0634},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peres-Neto, Jackson, Somers - 2003 - Giving meaningful interpretation to ordination axes Assessing loading significance in principal com.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2347--2363},
-title = {{Giving meaningful interpretation to ordination axes: Assessing loading significance in principal component analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/00-0634/abstract},
-volume = {84},
-year = {2003}
-}
-@article{Ricotta2015,
-abstract = {Rao developed the DISC dissimilarity coefficient to summarize the dissimilarity between pairs of plots based on species abundances and interspecies dissimilarities. In this paper, we review the potential of the DISC coefficient for assessing plot-to- plot phylogenetic dissimilarity. First, the relationship between plot-to-plot dissimilarity and additive beta diversity is discussed. Next, we show that additive diversity decomposition can be interpreted in terms of a sum of classical Euclidean distances. Based on this geometrical interpretation of additive diversity decomposition, we then suggest an alternative way for calculating an analog of the DISC coefficient directly from the centroids of two species plots in multivariate phylogenetic space. The key to this method is that the centroids can be easily calculated by applying a principal coordinate analysis (PCoA) to the corresponding species phylogenetic distances. Finally, to show the potential of the DISC coefficient for analyzing the relationship between community structure and ecosystem functioning, we used the proposed measure by comparing phylogenetic and functional changes in plant communities along a primary succession on a glacier foreland in northern Italy. Our results show that changes in Grime's CSR functional classification of plant assemblages as competitors (C), stress-tolerators (S) and ruderals (R) along the successional gradient are also reflected in phylogenetic changes, indicating that species sorting by environmental filtering tends to favor the co-occurrence of phylogenetically related species. From a more theoretical viewpoint, the relationship between the proposed measure and the DISC coefficient helps in shedding new light on the additive decomposition of biological diversity into alpha, beta and gamma components.},
-author = {Ricotta, Carlo and Bacaro, Giovanni and Caccianiga, Marco and Cerabolini, Bruno E. L. and Moretti, Marco},
-doi = {10.1016/j.baae.2014.10.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2015 - A classical measure of phylogenetic dissimilarity and its relationship with beta diversity.pdf:pdf},
-journal = {Basic and Applied Ecology},
-number = {1},
-pages = {10--18},
-title = {{A classical measure of phylogenetic dissimilarity and its relationship with beta diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1439179114001340},
-volume = {16},
-year = {2015}
-}
-@article{Chao2015,
-abstract = {1. The compositional complexity of an assemblage is not expressible as a single number; standard measures such as diversities (Hill numbers) and entropies (Renyi entropies and Tsallis entropies) vary in their order q which determines themeasures' emphasis on rare or common species. Ranking and comparing assemblages depend on the choice of q.Ratherthanselecting oneora fewmeasurestodescribe an assemblage, it is preferable to convey the complete story by presenting a continuous profile, a plot of diversity or entropy as a function of q = 0. This makes it easy to visually compare the compositional complexities ofmultiple assemblages and to judge the even- ness of the relative abundance distributions of the assemblages. In practice, the profile is plotted for all values of q from 0 to q = 3 or 4 (beyond which it generally changes little). 2. These profiles are usually generated by substituting species sample proportions into the complexity measures. However, this empirical approach typically underestimates the true profile for low values of q, because samples usually miss some of the assemblage's species due to under-sampling. Although bias-reductionmethods exist for individual measures of order q = 0, 1 and 2, there has been no analyticmethod that unifies these bias-corrected estimates into a continuous profile. 3. For incomplete sampling data, this work proposes a novel analytic method to obtain accurate, continuous, low-bias diversity and entropy profileswith focus on loworders of q (0 = q = 3).Our approach is based on refor- mulating the diversity and entropy of any order q in terms of the successive discovery rates of new species with respect to sample size, that is the successive slopes of the species accumulation curve. A bootstrap method is applied to obtain approximate variances of our proposed profiles and to construct the associated confidence intervals. 4. Extensive simulations fromtheoreticalmodels and real surveys showthat the proposed profiles greatly reduce under-sampling bias and have substantially lower bias and mean-squared error than the empirical profile, espe- cially for q = 1.Ourmethodisalsoextendedtodealwithincidence data.},
-author = {Chao, Anne and Jost, Lou},
-doi = {10.1111/2041-210X.12349},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Jost - 2015 - Estimating diversity and entropy profiles via discovery rates of new species.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {8},
-pages = {873--882},
-title = {{Estimating diversity and entropy profiles via discovery rates of new species}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12349/abstract},
-volume = {6},
-year = {2015}
-}
-@book{Cressie1993,
-address = {New York},
-author = {Cressie, Noel A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cressie - 1993 - Statistics for spatial data.pdf:pdf},
-isbn = {978-1-119-11461-1},
-pages = {1--900},
-publisher = {John Wiley {\&} Sons},
-title = {{Statistics for spatial data}},
-url = {http://www.wiley.com/WileyCDA/WileyTitle/productCd-1119114616.html},
-year = {1993}
-}
-@article{Hector2000,
-abstract = {Decomposition of plant litter is a key process for the flow of energy and nutrients in ecosystems that may be sensitive to the loss of biodiversity. Two hypothetical mechanisms by which changes in plant diversity could affect litter decomposition are (1) through changes in litter species composition, and (2) by altering the decomposition microenvironment. We tested these ideas in relation to the short-term decomposition of herbaceous plant litter in experimental plant assemblages that differed in the numbers and types of plant species and functional groups that they contained to simulate loss of plant diversity. We used different litterbag experiments to separate the two potential pathways through which diversity could have an effect on decomposition. Our two litterbag trials showed that altering plant diversity affected litter breakdown differently through changes in decomposition microenvironment than through changes in litter composition. In the decomposition microenvironment experiment there was a significant but weak decline in decomposition rate in relation to decreasing plant diversity but no significant effect of plant composition. The litter composition experiment showed no effect of richness but significant effects of composition, including large differences between plant species and functional groups in litter chemistry and decomposition rate. However, for a nested subset of our litter mixtures decomposition was not accurately predicted from single-species bags; there were positive, non-additive effects of litter mixing which enhanced decomposition. We critically assess the strengths and limitations of our short-term litterbag trials in predicting the longer-term effects of changes in plant diversity on litter decomposition rates.},
-author = {Hector, Andrew and Beale, A. J. and Minns, A. and Otway, S. J. and Lawton, John H.},
-doi = {10.1034/j.1600-0706.2000.900217.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hector et al. - 2000 - Consequences of the reduction of plant diversity for litter decomposition effects through litter quality and micr.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {357--371},
-title = {{Consequences of the reduction of plant diversity for litter decomposition: effects through litter quality and microenvironment}},
-url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2000.900217.x/abstract},
-volume = {90},
-year = {2000}
-}
-@incollection{Gabaix2004,
-abstract = {We review the accumulated knowledge on city size distributions and determinants of urban growth. This topic is of interest because of a number of key stylized facts, including notably Zipf's law for cities (which states that the number of cities of size greater than S is proportional to 1/S) and the importance of urban primacy. We first review the empirical evidence on the upper tail of city size distribution. We offer a novel discussion of the important econometric issues in the characterization of the distribution. We then discuss the theories that have been advanced to explain the approximate constancy of the distribution across very different economic and social systems, emphasizing both bare-bone statistical theories and more developed economic theories. We discuss the more recent work on the determinants of urban growth and, in particular, growth regressions, economic explanations of city size distributions other than Gibrat's law, consequences of major shocks (quasi natural experiments), and the dynamics of U.S. urban evolution.},
-address = {Amsterdam},
-author = {Gabaix, Xavier and Ioannides, Yannis M},
-booktitle = {Handbook of Urban and Regional Economics},
-doi = {10.1016/S1574-0080(04)80010-5},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gabaix, Ioannides - 2004 - The Evolution of City Size Distributions.pdf:pdf},
-pages = {2341--2378},
-publisher = {Elsevier. North Holland},
-title = {{The Evolution of City Size Distributions}},
-url = {http://www.sciencedirect.com/science/article/pii/S1574008004800105},
-year = {2004}
-}
-@article{McGill2003,
-abstract = {One of the fundamental questions of ecology is what controls biodiversity. Recent theory suggests that biodiversity is controlled predominantly by neutral drift of species. This theory has generated considerable controversy, because it claims that many mechanisms that have long been studied by ecologists (such as niches) have little involvement in structuring communities. The theory predicts that the species abundance distribution within a community should follow a zero-sum multinomial distribution (ZSM), but this has not, so far, been rigorously tested. Specifically, it remains to be shown that the ZSM fits the data significantly better than reasonable null models. Here I test whether the ZSM fits several empirical data sets better than the lognormal distribution. It does not. Not only does the ZSM fail to fit empirical data better than the lognormal distribution 95{\%} of the time, it also fails to fit empirical data better even a majority of the time. This means that there is no evidence that the ZSM predicts abundances better than the much more parsimonious null hypothesis.},
-annote = {10.1038/nature01583},
-author = {McGill, Brian J.},
-doi = {10.1038/nature01583},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McGill - 2003 - A test of the unified neutral theory of biodiversity.pdf:pdf},
-journal = {Nature},
-number = {6934},
-pages = {881--885},
-title = {{A test of the unified neutral theory of biodiversity}},
-url = {http://dx.doi.org/10.1038/nature01583},
-volume = {422},
-year = {2003}
-}
-@article{Ulanowicz2014,
-abstract = {Articulating what limits the length of trophic food chains has remained one of the most enduring challenges in ecology. Mere counts of ecosystem species and transfers have not much illumined the issue, in part because magnitudes of trophic transfers vary by orders of magnitude in power-law fashion. We address this issue by creating a suite of measures that extend the basic indexes usually obtained by counting taxa and transfers so as to apply to networks wherein magnitudes vary by orders of magnitude. Application of the extended measures to data on ecosystem trophic networks reveals that the actual complexity of ecosystem webs is far less than usually imagined, because most ecosystem networks consist of a multitude of weak connections dominated by a relatively few strong flows. Although quantitative ecosystem networks may consist of hundreds of nodes and thousands of transfers, they nevertheless behave similarly to simpler representations of systems with fewer than 14 nodes or 40 flows. Both theory and empirical data point to an upper bound on the number of effective trophic levels at about 3-4 links. We suggest that several whole-system processes may be at play in generating these ecosystem limits and regularities.},
-author = {Ulanowicz, Robert E. and Holt, Robert D. and Barfield, Michael},
-doi = {10.1111/ele.12216},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ulanowicz, Holt, Barfield - 2014 - Limits on ecosystem trophic complexity Insights from ecological network analysis.pdf:pdf},
-journal = {Ecology Letters},
-number = {2},
-pages = {127--136},
-title = {{Limits on ecosystem trophic complexity: Insights from ecological network analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12216/abstract},
-volume = {17},
-year = {2014}
-}
-@article{McGill2007,
-abstract = {Species abundance distributions (SADs) follow one of ecology's oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.},
-author = {McGill, Brian J. and Etienne, Rampal S. and Gray, John S. and Alonso, David and Anderson, Marti J. and Benecha, Habtamu Kassa and Dornelas, Maria and Enquist, Brian J. and Green, Jessica L. and He, Fangliang and Hurlbert, Allen H. and Magurran, Anne E. and Marquet, Pablo A. and Maurer, Brian A. and Ostling, Annette and Soykan, Candan U. and Ugland, Karl I. and White, Ethan P.},
-doi = {10.1111/j.1461-0248.2007.01094.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McGill et al. - 2007 - Species abundance distributions moving beyond single prediction theories to integration within an ecological fram.pdf:pdf},
-journal = {Ecology Letters},
-number = {10},
-pages = {995--1015},
-title = {{Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2007.01094.x},
-volume = {10},
-year = {2007}
-}
-@article{Retzer2009,
-abstract = {Publications are thought to be an integrative indicator best suited to measure the multifaceted nature of scientific performance. Therefore, indicators based on the publication record (citation analysis) are the primary tool for rapid evaluation of scientific performance. Nevertheless, it has to be questioned whether the indicators really do measure what they are intended to measure because people adjust to the indicator value system by optimizing their indicator rather than their performance. Thus, no matter how sophisticated an indicator may be, it will never be proof against manipulation. A literature review identifies the most critical problems of citation analysis: database-related problems, inflated citation records, bias in citation rates and crediting of multi-author papers. We present a step-by-step protocol to address these problems. By applying this protocol, reviewers can avoid most of the pitfalls associated with the pure numbers of indicators and achieve a fast but fair evaluation of a scientist's performance. We as ecologists should accept complexity not only in our research but also in our research evaluation and should encourage scientists of other disciplines to do so as well. (C) 2008 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.},
-annote = {ISI Document Delivery No.: 481VE
-Times Cited: 1
-Cited Reference Count: 61
-Retzer, Vroni Jurasinski, Gerald
-ELSEVIER GMBH, URBAN {\&} FISCHER VERLAG},
-author = {Retzer, Vroni and Jurasinski, Gerald},
-doi = {10.1016/j.baae.2008.09.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Retzer, Jurasinski - 2009 - Towards objectivity in research evaluation using bibliometric indicators - A protocol for incorporating comp.pdf:pdf},
-journal = {Basic and Applied Ecology},
-number = {5},
-pages = {393--400},
-title = {{Towards objectivity in research evaluation using bibliometric indicators - A protocol for incorporating complexity}},
-volume = {10},
-year = {2009}
-}
-@article{Zhu2007,
-abstract = {Geographic concentration of industries is the regional- ized distribution of some industries in certain areas, which focuses on the ratio of a certain industry to the whole industries (He and Liu, 2006). In this paper we explore the improved M function of geographic concentration that adds the parameter of the number of firms according to the definition of geographic concentration of industries. The spatial distribution of the main manufacturing industries of Lanzhou urban area is evaluated based on it. The results of the evaluation imply that the spatial distribution of the main manufacturing industries is more concentrated than that of others in Lanzhou and it can absorb lots of labor forces. But the incidence, competition ability and density of the distribution of enterprises are different for each single sector, and enterprises with different production features are located closely. And three main problems are discovered. Finally, three countermeasures are put forward: locating the industrial enterprises in urban areas in a proper way through planning and policies; adjusting the industrial structure of the inner city; strengthening the local rearrangement of the existing industrial concentration areas.},
-author = {Zhu, Shuang and Chen, Xiaojian},
-doi = {10.1080/10042857.2007.10677488},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhu, Chen - 2007 - Optimizing Urban Spatial Structure of Lanzhou Based on Geographic Concentration Method of Industries.pdf:pdf},
-journal = {Chinese Journal of Population, Resources and Environment},
-number = {1},
-pages = {58--62},
-title = {{Optimizing Urban Spatial Structure of Lanzhou Based on Geographic Concentration Method of Industries}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/10042857.2007.10677488},
-volume = {5},
-year = {2007}
-}
-@article{Jaffe1989,
-abstract = {The existence of geographically mediated "spillovers" from university research to commercial innovation is explored using state-level time-series data on corporate patents, corporate R{\&}D, and university research. A significant effect of university research on corporate patents is found, particularly in the areas of Drugs and Medical Technology, and Electronics, Optics, and Nuclear Technology. In addition, university research appears to have an indirect effect on local innovation by inducing industrial R{\&}D spending.},
-author = {Jaffe, Adam B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaffe - 1989 - Real Effects of Academic Research.pdf:pdf},
-journal = {The American Economic Review},
-number = {5},
-pages = {957--970},
-title = {{Real Effects of Academic Research}},
-url = {https://www.jstor.org/stable/1831431},
-volume = {79},
-year = {1989}
-}
-@article{Charles-Dominique2003,
-abstract = {Aims Astrocaryum sciophilum (Miq.) Pulle (Arecaceae) is an understorey palm, endemic to north-eastern South America with a patchy distribution. We tested the hypothesis that the spatial distribution of this palm species is not in equilibrium but is slowly colonizing the forest understorey. Location Inventories and seed dispersal studies were conducted in the undisturbed tropical forest close to the Nouragues research station, French Guiana. Additional data were collected in the entire territory of French Guiana. Methods We studied the demography of A. sciophilum on a 20-ha plot located at the edge of its distribution. The age of the palms was estimated by postulating an exponentially decreasing abundance by age class. Direct seed dispersal experiments were also conducted, to estimate dispersal parameters. The seeds of A. sciophilum were dispersed only by rodents. This information was used to parameterize a forest growth simulator, to study the spatial spread of this species. Results Within the sampling plot, the density of A. sciophilum dropped sharply from about 500 individuals per hectare to zero. The maturation age was estimated to be 170+/-70 years, and over 55 years with 95{\%} confidence. Seed-dispersal experiments yielded an average seed dispersal distance of 11 m and a maximum estimated dispersal distance of 125 m across a generational span of 55 years to maturity. Therefore, the maximal estimated colonization speed is 2.3 m/y. Conclusions Empirical results and numerical simulations suggest that the boundary of the A. sciophilum population is a colonization front, and that the range of this species is slowly expanding. The implications of this result in respect of palaeoenvironmental changes in this region are discussed.},
-annote = {Article
-English
-GLOBAL ECOL BIOGEOGR
-666NV},
-author = {Charles-Dominique, Pierre and Chave, J{\'{e}}r{\^{o}}me and Dubois, Marc-A. and {De Granville}, Jean-Jacques and Riera, Bernard and Vezzoli, C{\'{e}}cile},
-doi = {10.1046/j.1466-822X.2003.00020.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Charles-Dominique et al. - 2003 - Colonization front of the understorey palm Astrocaryum sciophilum in a pristine rain forest of French.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {3},
-pages = {237--248},
-title = {{Colonization front of the understorey palm Astrocaryum sciophilum in a pristine rain forest of French Guiana}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1466-822X.2003.00020.x/abstract},
-volume = {12},
-year = {2003}
-}
-@article{Gregorius2016a,
-abstract = {Dispersion and diversity are two variants of the notion of biological variation that are often not properly distinguished even though they address intrinsically disparate aspects. Dispersion focuses on the assessment of (variable) differences among individuals or types, while diversity focuses on the assessment of numbers of distinct types. Here, ‘type' is a proxy for biological entities such as species, genotype and phenotype culminating in individuals at the highest level of resolution. The present paper bridges the apparent gap between dispersion and diversity by showing how numbers of types and individuals can be treated as a dispersion characteristic (the number-characteristic). Drawing from the general concept of effective quantities, it is shown that the contribution of difference arrays to dispersion measures can always be summarized in terms of an effective difference. If the number-characteristic is realized in addition, numbers of types (of individuals) can be determined that are effectively distinct at specified levels of difference. Whereas measures of diversity that replace abundances of types by differences of each type from other types can also be considered as numbers of effectively different types, they do not explicitly involve levels of distinctness among types. By contrast, dispersion effective numbers of types gain their sole validity from explicit reference to the degree to which types effectively differ from each other. In particular, dispersion effective numbers obey the diversity criterion only at levels of distinctness equal to or greater than the effective difference in that they do not exceed the actual number of types and become equal to that number only for uniform type distributions. The corresponding ‘proper dispersion effective number' thus sets an upper limit to the effective number of types in a community and meets the characteristics of a diversity effective number. Examples are outlined that have broader application in phylogenetics, population genetics and ecology.},
-author = {Gregorius, Hans-Rolf and Kosman, Evsey},
-doi = {10.1111/2041-210X.12665},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius, Kosman - 2016 - On the notion of dispersion - from dispersion to diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {275--391},
-title = {{On the notion of dispersion - from dispersion to diversity}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12665},
-volume = {8},
-year = {2017}
-}
-@article{Webb2000,
-abstract = {Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees ({\^{a}}‰¥10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.},
-annote = {Cited By (since 1996): 205
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: AMNTA
-doi: 10.1086/303378
-Language of Original Document: English
-Correspondence Address: Webb, C.O.; Arnold Arboretum of Harvard Univ., Cambridge, MA 02138, United States; email: cwebb@oeb.harvard.edu},
-author = {Webb, Campbell O.},
-doi = {10.1086/303378},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Webb - 2000 - Exploring the phylogenetic structure of ecological communities An example for rain forest trees.pdf:pdf},
-journal = {American Naturalist},
-number = {2},
-pages = {145--155},
-title = {{Exploring the phylogenetic structure of ecological communities: An example for rain forest trees}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/303378},
-volume = {156},
-year = {2000}
-}
-@article{Riera1990,
-abstract = {Outre les esp{\`{e}}ces pionni{\`{e}}res {\'{e}}voqu{\'{e}}es plus haut, cette dynamique fait intervenir les plantes cicatricielles ou nomades, et les dryades, ou esp{\`{e}}ces s{\'{e}}dentaires, structurantes et de soutien. La mosa{\"{i}}que foresti{\`{e}}re d{\'{e}}pend des phases successives de cette mosa{\"{i}}que mais aussi des processus dont les plus importants sont la diss{\'{e}}mination et la dynamique de la croissance, s'exprimant naturellement quand interviennent des chablis},
-author = {Ri{\'{e}}ra, Bernard and Puig, Henri and Lescure, Jean-Paul},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ri{\'{e}}ra, Puig, Lescure - 1990 - La dynamique de la for{\^{e}}t naturelle.pdf:pdf},
-journal = {Bois et for{\^{e}}t des tropiques},
-pages = {69--78},
-title = {{La dynamique de la for{\^{e}}t naturelle}},
-url = {http://bft.cirad.fr/revues/notice{\_}fr.php?dk=416856},
-volume = {219},
-year = {1990}
-}
-@incollection{Barberousse2014,
-abstract = {Les taxonomistes ont pour vocation d'inventorier et de d{\'{e}}crire la biodiversit{\'{e}}, mais leur t{\^{a}}che colossale est de plus en plus difficile {\`{a}} r{\'{e}}aliser car ils sont de moins en moins nombreux. Ce n'est pas seulement la biodiversit{\'{e}} qui est en crise, mais bien aussi la taxonomie, qui peine {\`{a}} fournir les {\'{e}}l{\'{e}}ments n{\'{e}}cessaires {\`{a}} l'utilisation, par les autres biologistes, des noms d'esp{\`{e}}ces. Les techniques r{\'{e}}centes d'analyse g{\'{e}}n{\'{e}}tique vontelles permettre de surmonter la crise actuelle de la taxonomie ? L'enjeu de ce chapitre est de montrer {\`{a}} quelles conditions cela pourra {\^{e}}tre le cas. Nous pr{\'{e}}sentons le projet du Barcoding of Life qui a pour but de faciliter, et donc d'acc{\'{e}}l{\'{e}}rer le diagnostic des esp{\`{e}}ces en utilisant des caract{\`{e}}res mol{\'{e}}culaires relativement faciles {\`{a}} identifier. Nous montrons que l'efficacit{\'{e}} de cet instrument d{\'{e}}pend de fa{\c{c}}on cruciale de la bonne gestion des collections d'histoire naturelle, en raison de l'importance que rev{\^{e}}tent les sp{\'{e}}cimens conserv{\'{e}}s pour l'entreprise taxonomique. Nous proposons donc un {\'{e}}tat des lieux de la taxonomie au moment o{\`{u}} l'initiative du Barcoding of Life prend de l'ampleur.},
-address = {Paris},
-author = {Barberousse, Anouk and Samadi, Sarah},
-booktitle = {La biodiversit{\'{e}} en question. Enjeux philosophiques, {\'{e}}thiques et scientifiques},
-chapter = {6},
-editor = {Casetta, Elena and Delord, Julien},
-pages = {155--182},
-publisher = {Editions Mat{\'{e}}riologiques},
-title = {{La taxonomie et les collections d'histoire naturelle {\`{a}} l'heure de la sixi{\`{e}}me extinction}},
-year = {2014}
-}
-@article{Haffer1969,
-abstract = {Most species probably originated in forest refuges during dry climatic periods.},
-author = {Haffer, J{\"{u}}rgen},
-doi = {10.1126/science.165.3889.131},
-isbn = {1653889131},
-issn = {0036-8075},
-journal = {Science (New York, N.Y.)},
-number = {3889},
-pages = {131--137},
-pmid = {17834730},
-title = {{Speciation in Amazonian Forest Birds}},
-volume = {165},
-year = {1969}
-}
-@article{Cohen1968,
-author = {Cohen, Joel E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cohen - 1968 - Alternate Derivations of a Species-Abundance Relation.pdf:pdf},
-journal = {The American Naturalist},
-number = {924},
-pages = {165--172},
-title = {{Alternate Derivations of a Species-Abundance Relation}},
-volume = {102},
-year = {1968}
-}
-@book{Clements1916,
-address = {Washington, D.C.},
-author = {Clements, Frederic Edward},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clements - 1916 - Plant succession an analysis of the development of vegetation.pdf:pdf},
-publisher = {Carnegie Institution of Washington},
-title = {{Plant succession; an analysis of the development of vegetation}},
-year = {1916}
-}
-@article{Isserman1977,
-abstract = {This article presents a theoretical rationale for the use of location quotients in estimating regional economic impacts. Then it suggests a number of procedural modifications which are consistent with that underlying rationale. Two of the modifications are implemented and are shown to improve the accuracy of the multiplier. Previous empirical work, often cited as evidence of the inaccuracy of the location quotient approach, is found to be questionable itself. The paper concludes, in part, that the location quotient approach can be a useful planning tool.},
-author = {Isserman, Andrew M.},
-doi = {10.1080/01944367708977758},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Isserman - 1977 - The Location Quotient Approach for Estimating Regional Economic Impacts.pdf:pdf},
-journal = {Journal of the American Institute of Planners},
-number = {1},
-pages = {33--41},
-title = {{The Location Quotient Approach for Estimating Regional Economic Impacts}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/01944367708977758},
-volume = {43},
-year = {1977}
-}
-@article{Roberge2004,
-abstract = {In the face of limited funding, knowledge, and time for action, conservation efforts often rely on shortcuts for the maintenance of biodiversity. The umbrella species concept—proposed as a way to use species requirements as a basis for conservation planning—has recently received growing attention. We reviewed the literature to evaluate the concept's general usefulness. An umbrella species is defined as a species whose con- servation is expected to confer protection to a large number of naturally co-occurring species. This concept has been proposed as a tool for determining the minimum size for conservation areas, selecting sites to be included in reserve networks, and setting minimum standards for the composition, structure, and processes of ecosystems. Among the species suggested as potential umbrellas, most are large mammals and birds, but invertebrates are increasingly being considered. Eighteen research papers, most of which were based on hypo- thetical reserves or conservation networks, have provided evaluations of umbrella species schemes. These show that single-species umbrellas cannot ensure the conservation of all co-occurring species because some species are inevitably limited by ecological factors that are not relevant to the umbrella species. Moreover, they provide evidence that umbrella species from a given higher taxonmay not necessarily confer protection to assemblages from other taxa. On the other hand, multi-species strategies based on systematic selection procedures (e.g., the focal species approach) offer more compelling evidence of the usefulness of the concept. Evaluations of um- brella species schemes could be improved by including measures of population viability and data from many years, as well as by comparing the efficiency of the proposed scheme with alternative management strategies.},
-author = {Roberge, Jean-Michel and Angelstam, Per},
-doi = {10.1111/j.1523-1739.2004.00450.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roberge, Angelstam - 2004 - Usefulness of the Umbrella Species Concept.pdf:pdf},
-journal = {Conservation Biology},
-number = {1},
-pages = {76--85},
-title = {{Usefulness of the Umbrella Species Concept as a Conservation Tool}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2004.00450.x/full},
-volume = {18},
-year = {2004}
-}
-@article{Diggle1978,
-abstract = {In a recent paper, Ripley (1977) discusses the use of two goodness-of-fit criteria for spatial point pattern data. Both criteria can be adapted to the associated problem of parameter estimation. To illustrate their use in this respect, we rework one of Ripley's examples and reach rather different conclusions.},
-author = {Diggle, Peter J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle - 1978 - On Parameter Estimation for Spatial Point Processes.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {178--181},
-title = {{On Parameter Estimation for Spatial Point Processes}},
-url = {https://www.jstor.org/stable/2984752},
-volume = {40},
-year = {1978}
-}
-@article{Dumais2002,
-abstract = {The degree of geographic concentration of individual manufacturing industries in the U.S. has declined only slightly in the last twenty years. At the same time, new plant births, plant expansions, contractions and closures have shifted large quantities of employment across plants, firms, and locations. This paper uses data from the Census Bureau's Longitudinal Research Database to examine how relatively stable levels of geographic concentration emerge from this dynamic process. While industries' agglomeration levels tend to remain fairly constant, we find that there is greater variation in the locations of these agglomerations. We then decompose aggregate concentration changes into portions attributable to plant births, expansions, contractions, and closures, and find that the location choices of new firms and differences in growth rates have played the most significant role in reducing levels of geographic concentration, while plant closures have tended to reinforce agglomeration. Finally, we look at coagglomeration patterns to test three of Marshall's theories of industry agglomeration: (1) agglomeration saves transport costs by proximity to input suppliers or final consumers, (2) agglomeration allows for labor market pooling, and (3) agglomeration facilitates intellectual spillovers. While there is some truth behind all three theories, we find that industrial location is far more driven by labor mix than by any of the other explanatory variables.},
-author = {Dumais, Guy and Ellison, Glenn and Glaeser, Edward L},
-doi = {10.1162/003465302317411479},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dumais, Ellison, Glaeser - 2002 - Geographic concentration as a dynamic process.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {2},
-pages = {193--204},
-title = {{Geographic concentration as a dynamic process}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/003465302317411479},
-volume = {84},
-year = {2002}
-}
-@article{Paninski2003,
-abstract = {We present some new results on the nonparametric estimation of entropy and mutual information. First, we use an exact local expansion of the entropy function to prove almost sure consistency and central limit theorems for three of the most commonly used discretized information estimators. The setup is related to Grenander's method of sieves and places no assumptions on the underlying probability measure generating the data. Second, we prove a converse to these consistency theorems, demonstrating that a misapplication of the most common estimation techniques leads to an arbitrarily poor estimate of the true information, even given unlimited data. This “inconsistency” theorem leads to an analytical approximation of the bias, valid in surprisingly small sample regimes and more accurate than the usual formula of Miller and Madow over a large region of parameter space. The two most practical implications of these results are negative: (1) information estimates in a certain data regime are likely contaminated by bias, even if “bias-corrected” estimators are used, and (2) confidence intervals calculated by standard techniques drastically underestimate the error of the most common estimation methods. Finally, we note a very useful connection between the bias of entropy estimators and a certain polynomial approximation problem. By casting bias calculation problems in this approximation theory framework, we obtain the best possible generalization of known asymptotic bias results. More interesting, this framework leads to an estimator with some nice properties: the estimator comes equipped with rigorous bounds on the maximum error over all possible underlying probability distributions, and this maximum error turns out to be surprisingly small. We demonstrate the application of this new estimator on both real and simulated data.},
-author = {Paninski, Liam},
-doi = {10.1162/089976603321780272},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Paninski - 2003 - Estimation of Entropy and Mutual Information.pdf:pdf},
-journal = {Neural Computation},
-number = {6},
-pages = {1191--1253},
-title = {{Estimation of Entropy and Mutual Information}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/089976603321780272},
-volume = {15},
-year = {2003}
-}
-@article{Maurel1997a,
-author = {Maurel, Fran{\c{c}}oise},
-journal = {Economie et Pr{\'{e}}vision},
-number = {5},
-pages = {i--iii},
-title = {{Contributions {\`{a}} la nouvelle {\'{e}}conomie g{\'{e}}ographique: pr{\'{e}}sentation g{\'{e}}n{\'{e}}rale}},
-volume = {131},
-year = {1997}
-}
-@article{Bersier2002,
-abstract = {A food web customarily describes the qualitative feeding relationships in a community. Descriptors have been used to extract ecologically meaningful information from such data, e.g., the proportion of top species (the proportion of taxa without consumers) or vulnerability (the average number of consumers per taxon). Analyses of collections of food webs based on these properties have revealed regularities that fostered the formulation of models of food-web structure. However, it has been shown that most of these qualitative descriptors are highly sensitive to the varying levels of sampling effort used to document a food web. The principal problem is that webs described extensively include trophic links of highly uneven magnitude, with typically few strong/important links and a wealth of weak ones; with qualitative descriptors, the same weight is given to all trophic interactions. To overcome this problem, food webs should be described and analyzed quantitatively. Consequently, we propose here a suite of food-web descriptors, which are built on information-theory indices and take the magnitude of the trophic interactions into account. We define descriptors having a similar meaning as the classical qualitative indices. Two versions of each quantitative descriptor are proposed, one giving the same weight to each taxon, and one weighting each taxon by the total amount of its incoming and outgoing biomass flows. We use a published quantitative food web to exemplify the computation of the new descriptors, and discuss their potential and limitations.},
-author = {Bersier, Louis-F{\'{e}}lix and Bana{\v{s}}ek-Richter, Carolin and Cattin, Marie-France},
-doi = {10.1890/0012-9658(2002)083[2394:QDOFWM]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bersier, Bana{\v{s}}ek-Richter, Cattin - 2002 - Quantitative descriptors of food-web matrices.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2394--2407},
-title = {{Quantitative descriptors of food-web matrices}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2002)083[2394:QDOFWM]2.0.CO;2/abstract},
-volume = {83},
-year = {2002}
-}
-@book{Losch1940,
-author = {L{\"{o}}sch, A.},
-edition = {(translati},
-publisher = {Yale University Press},
-title = {{The Economics of Location}},
-year = {1940}
-}
-@article{Bacaro2007a,
-abstract = {Plant communities are generally spatially structured. Therefore, in order to enhance the interpretation of distance-dependent community patterns, spatially explicit measures of $\beta$-diversity are needed that, besides simple species turnover, are able to account for the rate at which biological similarity decays with increasing distance. We show that a multivariate semivariogram computed from species presence and absenge data can be considered as a space-dependent alternative to existing definitions of $\beta$-diversity. To illustrate how the proposed method works, we used a classical data set from a second-growth piedmont hardwood forest. {\textcopyright} Akad{\'{e}}miai Kiad{\'{o}}, Budapest.},
-annote = {Cited By (since 1996):24
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: CEOCA
-Language of Original Document: English
-Correspondence Address: Bacaro, G.; Department of Environment Science G. Sarfatti, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy; email: bacaro@unisi.it},
-author = {Bacaro, Giovanni and Ricotta, Carlo},
-doi = {10.1556/ComEc.8.2007.1.6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro, Ricotta - 2007 - A spatially explicit measure of beta diversity.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {41--46},
-title = {{A spatially explicit measure of beta diversity}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34447578782{\&}partnerID=40{\&}md5=05fb73aeec651fcde6f66abee5fd21d4},
-volume = {8},
-year = {2007}
-}
-@article{Kuusinen1999,
-abstract = {The spatial pattern and occurrence of a threatened bryophyte, Neckera pennata, were studied in relation to the abundance and pattern of suitable substrate trees at two spatial scales: (1) in a 4x4 km fraction of fragmented, mostly managed southern boreal forest landscape, and (2) in an old-growth forest stand within this landscape, with abundant occurrence of suitable habitats. To explore in detail the spatial clustering of N. pennata at the forest stand scale, we applied a second order point process analysis based on the Ripley's K-function for binary point patterns. Neckera pennata proved to be a rare species in the studied landscape: it was found only on 31 Populus tremula trees. At the landscape scale, the distribution of the species was highly aggregated: the species occurred only within a 60 ha old-growth forest patch in the whole area. At the forest stand scale, N. pennata proved to be a widespread, randomly distributed species without any tendency towards aggregation. It was found on 19 Populus trees, which was only 1.5{\%} of the total 1253 potential substrate trees within the inventory area. The species showed a statistically significant preference towards large trees. The future of the species in the study area is unclear due to the very low population density and the lack of regeneration of Populus within the protected old-growth forest area hosting the remaining population.},
-author = {Kuusinen, Mikko and Penttinen, Antti},
-doi = {10.1111/j.1600-0587.1999.tb00522.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kuusinen, Penttinen - 1999 - Spatial pattern of the threatened epiphytic bryophyte Neckera pennata at two scales in a fragmented boreal.pdf:pdf},
-journal = {Ecography},
-number = {6},
-pages = {729--735},
-title = {{Spatial pattern of the threatened epiphytic bryophyte Neckera pennata at two scales in a fragmented boreal forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.1999.tb00522.x/full},
-volume = {22},
-year = {1999}
-}
-@article{Okie2015,
-abstract = {The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower tempera- tures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to con- trastinga- andb-diversity patterns. In accord with the predictions,a-diversity, niche widths and occupancies decreased while b-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between a-diversity and pH and a negative relationship between a-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms. 1.},
-author = {Okie, Jordan G. and Horn, David J. Van and Storch, David and Barrett, John E. and Gooseff, Michael N. and Kopsova, Lenka and Takacs-Vesbach, Cristina D. and Okie, Jordan G.},
-doi = {10.1098/rspb.2014.2630},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Okie et al. - 2015 - Niche and metabolic principles explain patterns of diversity and distribution theory and a case study with soil ba.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {20142630},
-title = {{Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities}},
-url = {http://dx.doi.org/10.1098/rspb.2014.2630},
-volume = {282},
-year = {2015}
-}
-@article{Condit2012,
-abstract = {The neutral theory of community ecology can predict diversity and abundances of tropical trees, but only under the assumption of steady input of new species into the community. Without input, diversity of a neutral community collapses, so the theory's predictions are not relevant unless novel species evolve or immigrate. We derive analytically the species input needed to maintain a target tree diversity, and find that a rate close to 1.0 x 10(-4) per recruit would maintain the observed diversity of 291 species in the Barro Colorado 50-ha tree plot in Panama. We then measured the rate empirically by comparing species present in one complete enumeration of the plot to those present five years later. Over six census intervals, the observed rate of input was 0.6 x 10(-4) to 1.8 x 10(-4) species per recruit, suggesting that there is adequate immigration of novel species to maintain diversity. Species interactions, niche partitioning, or density-dependence, while they may be present, do not appear to enhance tree species richness at Barro Colorado.},
-author = {Condit, Richard and Chisholm, Ryan A. and Hubbell, Stephen P.},
-doi = {10.1371/journal.pone.0049826},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Condit, Chisholm, Hubbell - 2012 - Thirty Years of Forest Census at Barro Colorado and the Importance of Immigration in Maintaining Dive.PDF:PDF},
-journal = {PLoS ONE},
-number = {11},
-pages = {e49826},
-title = {{Thirty Years of Forest Census at Barro Colorado and the Importance of Immigration in Maintaining Diversity}},
-volume = {7},
-year = {2012}
-}
-@article{Colwell1971,
-abstract = {Measures of niche breadth and overlap that depend on the distribution of individuals among resource states (ecological categories) should be independent of the relative abundance of the species and of the number of resource states considered. Such measures should also take into account the degree of distinctness of the resource states from the point of view of the organisms concerned. An ecoassay of the distinctness of resource states may well be easier and more meaningful than measurements of physical and chemical factors. We propose that the species composition of communities utilizing different resource states may be used to develop weighting factors with which each state may be weighted in proportion to its degree of distinctness. The weighting factors are used in the development of indices of niche breadth and overlap that correct for variation in the range and distinctness of resource states and that suffer less from human subjectivity than do the measures used to date. The use of such indices and the relationship of niche overlap to competition are discussed.},
-author = {Colwell, Robert K. and Futuyma, Douglas J.},
-doi = {10.2307/1934144},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Colwell, Futuyma - 1971 - On the measurement of noche breadth and overlap.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {567--576},
-title = {{On the measurement of niche breadth and overlap}},
-url = {https://www.jstor.org/stable/1934144},
-volume = {52},
-year = {1971}
-}
-@article{Hanus1998,
-abstract = {Reconstruction of the spatial pattern of trees is important for the accurate visual display of unmapped stands. The proposed process for generating the spatial pattern is a nonsimple sequential inhibition process, with the inhibition zone proportionate to the scaled maximum crown width of an open- grown tree of the same species and same diameter at breast height as the subject tree. The results of this coordinate generation procedure are compared with mapped stem data from 9 natural stands of Douglas fir (Pseudotsuga menziesii) at 2 ages, using a transformed Ripley's K(d) function (Ripley's method counts the number of trees with a random location within each point pattern). The stands used in the analysis were naturally regenerated, and from 3 locations in the Coast Range of Oregon; the 2 age measurements analysed were 25-38 yr apart (starting at ages from 20 to 47 yr). The results of this comparison indicate that the proposed method, based on complete tree lists, successfully replicated the spatial patterns of the trees in all nine stands at both ages and over the range of distances examined. On the basis of these findings and the procedure's ability to model effects through time, the nonsimple sequential inhibition process has been chosen to generate tree coordinates in the VIZ4ST computer program for displaying forest stand structure in naturally regenerated young Douglas-fir stands.},
-author = {Hanus, Mark L and Hann, David W and Marshall, David D},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hanus Hann and Marshall FS 1998.pdf:pdf},
-journal = {Forest Science},
-number = {1},
-pages = {125--133},
-title = {{Reconstructing the spatial pattern of trees from routine stand examination measurements}},
-url = {https://pubs.er.usgs.gov/publication/1016509},
-volume = {44},
-year = {1998}
-}
-@article{Perry1995,
-abstract = {1. A new method of quantifying spatial pattern was introduced for two-dimensional mapped data, with an associated index of aggregation and a test for departures from randomness, based on an attractive algorithm in which individuals in the sample move to a regular arrangement which resembles a hexagonal lattice, using Voronoi tessellations. The algorithm incorporates a biological model for the dispersal of individuals from a source, in which each individual is assigned a dynamic territory. The method is one of a class known as Spatial Analysis by Distance IndicEs (SADIE). 2. Two diagnostic plots were introduced, each based on the distance of the sample from the final, regular arrangement, to aid the description of the observed spatial pattern. 3. By backtracking from the observed sample points away from the final arrangement, the presence of clusters in the sample may be detected more easily, and heuristic estimates derived of the cluster foci. 4. Examples are given for seven sets of data, with analyses of over 20 subsets at several spatial scales, concerning: aphids, beetle larvae, ant mounds, sparrowhawk nesting territories, pine seedlings, redwood seedlings, and biological cells.},
-author = {Perry, Joe N.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Perry - 1995 - Spatial Analysis by Distance Indices.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {3},
-pages = {303--314},
-title = {{Spatial Analysis by Distance Indices}},
-volume = {64},
-year = {1995}
-}
-@article{Henderson2001,
-abstract = {Economic development and underdevelopment is one aspect of the uneven spatial distribution of economic activity. This paper reviews existing literature on geography and development, and argues that rigorous theoretical and empirical analysis is needed to increase understanding of the role of geography in development and to better design development policy. The analytical issues are: why does economic activity cluster in centers of activity? How do new centers develop? And what are the consequences of remoteness from existing centers? Empirical evidence comes both from the international context and from studies of internal economic geography and urbanization.},
-author = {Henderson, J. Vernon and Shalizi, Zmarak and Venables, Anthony J.},
-doi = {10.1093/jeg/1.1.81},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Henderson, Shalizi, Venables - 2001 - Geography and development.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {1},
-pages = {81--105},
-title = {{Geography and development}},
-url = {https://doi.org/10.1093/jeg/1.1.81},
-volume = {1},
-year = {2001}
-}
-@article{Guermond1999,
-abstract = {La mesure est n{\'{e}}cessaire {\`{a}} l'approche scientifique. Des m{\'{e}}thodes de mesure appropri{\'{e}}es peuvent {\^{e}}tre mises en {\oe}uvre dans des domaines vari{\'{e}}s de la g{\'{e}}ographie tels que la localisation optimale d'un service public, le dessin d'un r{\'{e}}seau de transport, les SIG pour la gestion de l'environnement ou la simulation de politiques, etc. Le biais r{\'{e}}sultant du choix de tels programmes de recherche n'est pas imm{\'{e}}diatement perceptible, mais peut conduire {\`{a}} une inaptitude de la g{\'{e}}ographie {\`{a}} r{\'{e}}pondre aux probl{\`{e}}mes essentiels de la soci{\'{e}}t{\'{e}}. Ces r{\'{e}}ponses demandent un effort, au-del{\`{a}} des m{\'{e}}thodes de recherche, pour imaginer des r{\'{e}}ponses scientifiques qui permettent de rendre compte des pr{\'{e}}occupations de la soci{\'{e}}t{\'{e}}. C'est particuli{\`{e}}rement vrai pour la s{\'{e}}gr{\'{e}}gation spatiale et sociale dans les agglom{\'{e}}rations urbaines. La g{\'{e}}ographie «pure» s' oppose- t-elle {\`{a}} la g{\'{e}}ographie «sociale»?},
-author = {Guermond, Yves and Lajoie, Gilles},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guermond, Lajoie - 1999 - De la mesure en g{\'{e}}ographie sociale.pdf:pdf},
-journal = {L'Espace g{\'{e}}ographique},
-number = {1},
-pages = {84--90},
-title = {{De la mesure en g{\'{e}}ographie sociale}},
-url = {http://www.persee.fr/doc/spgeo{\_}0046-2497{\_}1999{\_}num{\_}28{\_}1{\_}1223},
-volume = {28},
-year = {1999}
-}
-@article{Kim2000,
-abstract = {In this paper we investigate industry characteristics associated with the clustering of establishments in three-digit SIC manufacturing industries in nonmetropolitan areas. The dispersion parameter k of the negative binomial distribution is selected as the measure of industry spatial concentration. Associations between industry characteristics and spatial concentration are investigated using OLS regression analysis. Our findings indicate that the spatial clustering of establishments is positively related to industry average establishment size, reliance on natural resource inputs, labor intensity, cost shares of professional and technical employees, and cost shares of low-skilled workers. Agglomeration is negatively related to multiplant structure, employment in precision production, and reliance on local product and input markets.},
-author = {Kim, Yunsoo and Barkley, David L. and Henry, Mark S.},
-doi = {10.1111/0022-4146.00173},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kim, Barkley, Henry - 2000 - Industry characteristics linked to establishment concentrations in nonmetropolitan areas.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {2},
-pages = {231--259},
-title = {{Industry characteristics linked to establishment concentrations in nonmetropolitan areas}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/0022-4146.00173/abstract},
-volume = {40},
-year = {2000}
-}
-@article{Audretsch1996,
-author = {Audretsch, David B. and Feldman, Maryann P.},
-doi = {10.1023/A:1021490715660},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Audretsch, Feldman - 1996 - R{\&}D Spillovers and the Geography of Innovation and Production.pdf:pdf},
-journal = {The American Economic Review},
-number = {3},
-pages = {630--640},
-title = {{R{\&}D Spillovers and the Geography of Innovation and Production}},
-url = {https://www.jstor.org/stable/2118216},
-volume = {86},
-year = {1996}
-}
-@book{Wiegand2014,
-abstract = {Understand How to Analyze and Interpret Information in Ecological Point Patterns Although numerous statistical methods for analyzing spatial point patterns have been available for several decades, they haven't been extensively applied in an ecological context. Addressing this gap, Handbook of Spatial Point-Pattern Analysis in Ecology shows how the techniques of point-pattern analysis are useful for tackling ecological problems. Within an ecological framework, the book guides readers through a variety of methods for different data types and aids in the interpretation of the results obtained by point-pattern analysis. Ideal for empirical ecologists who want to avoid advanced theoretical literature, the book covers statistical techniques for analyzing and interpreting the information contained in ecological patterns. It presents methods used to extract information hidden in spatial point-pattern data that may point to the underlying processes. The authors focus on point processes and null models that have proven their immediate utility for broad ecological applications, such as cluster processes. Along with the techniques, the handbook provides a comprehensive selection of real-world examples. Most of the examples are analyzed using Programita, a continuously updated software package based on the authors' many years of teaching and collaborative research in ecological point-pattern analysis. Programita is tailored to meet the needs of real-world applications in ecology. The software and a manual are available online.},
-author = {Wiegand, Thorsten and Moloney, Kirk A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand, Moloney - 2013 - Handbook of Spatial Point-Pattern Analysis in Ecology.pdf:pdf},
-isbn = {9781420082555},
-publisher = {Chapman and Hall/CRC},
-title = {{Handbook of Spatial Point-Pattern Analysis in Ecology}},
-year = {2013}
-}
-@article{deBello2009,
-abstract = {Questions: Trait differentiation among species occurs at different spatial scales within a region. How does the partitioning of functional diversity help to identify different community assembly mechanisms? Location: Northeastern Spain. Methods: Functional diversity can be partitioned into within-community (a) and among-communities (b) components, in analogy to Whittaker's classical a and b species diversity concept. In light of ecological null models, we test and discuss two algorithms as a framework to measure a and b functional diversity (the Rao quadratic entropy index and the variance of trait values). Species and trait (specific leaf area) data from pastures under different climatic conditions in NE Spain are used as a case study. Results: The proposed indices show different mathematical properties but similarly account for the spatial components of functional diversity. For all vegetation types along the climatic gradient, the observed a functional diversity was lower than expected at random, an observation consistent with the hypothesis of trait convergence resulting from habitat filtering. On the other hand, our data exhibited a remarkably higher functional diversity within communities compared to among communities (a {\textgreater}{\textgreater} b). In contrast to the high species turnover, there was a limited functional diversity turnover among communities, and a large part of the trait divergence occurred among coexisting species. Conclusions: Partitioning functional diversity within and among communities revealed that both trait convergence and divergence occur in the formation of assemblages from the local species pool. A considerable trait convergence exists at the regional scale in spite of changes in species composition, suggesting the existence of ecological redundancy among communities.},
-author = {de Bello, Francesco and Thuiller, Wilfried and Lep{\v{s}}, Jan and Choler, Philippe and Cl{\'{e}}ment, Jean Christophe and Macek, Petr and Sebasti{\`{a}}, Maria Teresa and Lavorel, Sandra},
-doi = {10.1111/j.1654-1103.2009.01042.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Bello et al. - 2009 - Partitioning of functional diversity reveals the scale and extent of trait convergence and divergence.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {475--486},
-title = {{Partitioning of functional diversity reveals the scale and extent of trait convergence and divergence}},
-volume = {20},
-year = {2009}
-}
-@article{Michaelis1913,
-author = {Michaelis, L. and Menten, Maud L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Michaelis, Menten - 1913 - Die Kinetik der Invertinwirkung.pdf:pdf},
-journal = {Biochemische Zeitschrift},
-pages = {333--369},
-title = {{Die Kinetik der Invertinwirkung}},
-url = {https://www.ncbi.nlm.nih.gov/pubmed/21888353},
-volume = {49},
-year = {1913}
-}
-@article{Ricotta2003b,
-abstract = {The degree to which abundances are divided equitably among community species or evenness is a basic property of any biological community. Several evenness indices have thus far been proposed in ecological literature. However, despite its vast potential applicability in ecological research, none seems to be generally preferred. Furthermore, only very few parametric evenness families have thus far been proposed. While traditional evenness indices supply point descriptions of community evenness, according to a parametric evenness family E({\^{I}}±), there is a continuum of possible evenness measures that differ in their sensitivity to changes in the relative abundances of dominant and rare species as a function of the parameter {\^{I}}±. In this review, I first summarize the basic requirements that a parametric evenness measure should meet to adequately behave in ecological studies. Next, I discuss the major drawbacks of these requirements and propose some alternative solutions. {\^{A}}{\textcopyright} 2003 Elsevier Science Ltd. All rights reserved.},
-annote = {Cited By (since 1996): 15
-Export Date: 28 December 2011
-Source: Scopus
-CODEN: JTBIA
-doi: 10.1016/S0022-5193(03)00026-2
-PubMed ID: 12727454
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, Rome 00185, Italy; email: carlo.ricotta@uniromal.it},
-author = {Ricotta, Carlo},
-doi = {10.1016/S0022-5193(03)00026-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2003 - On parametric evenness measures.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {2},
-pages = {189--197},
-title = {{On parametric evenness measures}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519303000262},
-volume = {222},
-year = {2003}
-}
-@book{Ripley1988,
-author = {Ripley, Brian D.},
-publisher = {Cambridge University Press},
-title = {{Statistical inference for spatial processes}},
-year = {1988}
-}
-@article{Coleman1981,
-abstract = {Consider a collection C of individuals from several species residing ina region R which is the union of a number of nonoverlapping subregions. Let ni be the number of individuals from species i which belong to C and hence reside somewhere in R. The simplest hypothesis about the spatial distribution throughout R of the members of C is that their placement in dwelling sites is random and noninteractive, with the probability of a given individual of C residing in a particular subregion r of R equal to the ratio $\alpha$ ofthe area of r to the area of R. It is shown here that when this hypothesis of random placement holds, the mean s̄ and variance $\sigma$2 of the number of species from C represented in r are given by explicit functions of $\alpha$, provided the number ni are known. Thus, if all the species in C have been censured, species-area data permit a test of the hypothesis of random placement. The nature of the dependence of s̄ and $\sigma$2 on $\alpha$ is discussed in detail for special cases in which the numbers ni are given by such theoritical abundance relations as the logarithmic series distribution, the “broken stick” distribution, the lognormal distribution, the Poisson lognormal distribution, and the gamma distribution. The arguments employed here to deduce consequences of the hypothesis of random choice are rigorous and exact. No use is made of the assumption, commonly made heretofore (but not in general correct, even under the hypothesis of random placement), that a species-area curve (giving the number of species expected to be found in a sample of known area) must have the same form as the corresponding collector's curve (giving the number of species expected in a sample of a known number of individuals). Nor is it assumed in advance, as is often done in the theory of island biogeography, that the distribution of individuals throughout the subregions of R is such thatthe species abundance relations for subregions of different areas must be of a preassigned type, i.e., must share a common form, such as that associated with a truncated lognormal distribution.},
-author = {Coleman, Bernard D.},
-doi = {10.1016/0025-5564(81)90086-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coleman - 1981 - On random placement and species-area relations.pdf:pdf},
-journal = {Mathematical Biosciences},
-number = {3-4},
-pages = {191--215},
-title = {{On random placement and species-area relations}},
-url = {https://doi.org/10.1016/0025-5564(81)90086-9},
-volume = {54},
-year = {1981}
-}
-@article{Szapudi1998,
-abstract = {A class of improved estimators is proposed for N-point correlation functions of galaxy clustering and for discrete spatial random processes in general. In the limit of weak clustering, the variance of the unbiased estimator converges to the continuum value much faster than with any alternative, and all terms giving rise to a slower convergence exactly cancel. Explicit variance formulae are provided for both Poisson and multinomial point processes using techniques for spatial statistics reported by Ripley. The formalism naturally includes most previously used statistical tools such as N-point correlation functions and their Fourier counterparts, moments of counts in cells, and moment correlators. For all these, and perhaps some other statistics, our estimator provides a straightforward means for efficient edge corrections.},
-annote = {Article
-English
-ASTROPHYS J
-2
-YY522},
-author = {Szapudi, Istv{\'{a}}n and Szalay, Alexander S},
-doi = {10.1086/311146},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Szapudi, Szalay - 1998 - A new class of estimators for the N-point correlations.pdf:pdf},
-journal = {Astrophysical Journal},
-number = {1},
-pages = {L41--L44},
-title = {{A new class of estimators for the N-point correlations}},
-url = {http://iopscience.iop.org/article/10.1086/311146},
-volume = {494},
-year = {1998}
-}
-@article{Webb2008,
-abstract = {Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. Capabilities: Phylocom calculates numerous metrics of phyloge- netic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows. Availability: Open source at: http://phylodiversity.net/phylocom/ Contact: cwebb@oeb.harvard.edu 1},
-author = {Webb, Campbell O. and Ackerly, David D. and Kembel, Steven W.},
-doi = {10.1093/bioinformatics/btn358},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Webb, Ackerly, Kembel - 2008 - Phylocom Software for the analysis of phylogenetic community structure and trait evolution.pdf:pdf},
-journal = {Bioinformatics},
-number = {18},
-pages = {2098--2100},
-title = {{Phylocom : Software for the analysis of phylogenetic community structure and trait evolution}},
-url = {bioinformatics.oxfordjournals.org/content/24/18/2098.short},
-volume = {24},
-year = {2008}
-}
-@article{Jones1994,
-abstract = {Interactions between organisms are a major determinant of the distribution and abundance of species. Ecology textbooks (e.g., Ricklefs 1984, Krebs 1985, Begon et al. 1990) summarise these important interactions as intra- and interspecific competition for abiotic and biotic resources, predation, parasitism and mutualism. Conspicuously lacking from the list of key processes in most text books is the role that many organisms play in the creation, modification and maintenance of habitats. These activities do not involve direct trophic interactions between species, but they are nevertheless important and common. The ecological literature is rich in examples of habitat modification by organisms, some of which have been extensively studied (e.g. Thayer 1979, Naiman et al. 1988).},
-author = {Jones, Clive G. and Lawton, John H. and Shachak, Moshe},
-doi = {10.1007/978-1-4612-4018-1_14},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jones, Lawton, Shachak - 1994 - Organisms as Ecosystem Engineers.pdf:pdf},
-journal = {Oikos,},
-number = {3},
-pages = {373--386},
-title = {{Organisms as Ecosystem Engineers}},
-url = {https://link.springer.com/chapter/10.1007{\%}2F978-1-4612-4018-1{\_}14},
-volume = {69},
-year = {1994}
-}
-@article{Aiginger2000,
-abstract = {This paper is about structural change within European Manufacturing since 1985, thereby covering the key period in the ongoing processes of European integration and world wide globalisation. It focuses on whether the Member States are becoming more specialised in their industrial structures, and, if so, whether this means that industries are also becoming more geographically concentrated within the European Union. Perhaps counter-intuitively, we find that, although specialisation has indeed increased, concentration has moved in the opposite direction. In order to explain this, we derive a formal relationship between the two concepts which shows how increasing industrial specialisation has been offset by faster growth by the smaller Member States, with the net effect that industries have become somewhat less geographically concentrated. We suggest one potential theoretical explanation by drawing upon recent work by Fujita, Krugman and Venables (1999)},
-author = {Aiginger, Karl and Davies, Stephen W},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Aiginger, Davies - 2003 - Industrial Specialisation and Geographic Concentration two sides of the same coin Not for the European Union.pdf:pdf},
-journal = {Journal of Applied Economics},
-number = {2},
-pages = {231--248},
-title = {{Industrial Specialisation and Geographic Concentration: two sides of the same coin? Not for the European Union}},
-volume = {7},
-year = {2003}
-}
-@article{Hubalek2000,
-abstract = {Twenty-four measures of species diversity, richness and equitability were compared using both real species abundance data (bird censuses on a standard study plot) and simple simulation tests. Based on 20 criteria, the most recommendable measures for the estimation of alpha diversity of species have been Fager's "number of moves per specimen", exponential Shannon's information (or H'), reciprocal Simpson's lambda, and species richness (number of species). However. the last index is only appropriate when sample sizes are approximately equal otherwise it can be misleading and Hurlbert's rarefaction method should be applied. The other measures tested, especially all equitability indices, have been shown to be problematic and should not be used regularly for the measurement of species diversity.},
-author = {Hubalek, Zden{\v{e}}k},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hubalek - 2000 - Measures of species diversity in ecology an evaluation.pdf:pdf},
-journal = {Folia Zoologica},
-number = {4},
-pages = {241--260},
-title = {{Measures of species diversity in ecology: an evaluation}},
-volume = {49},
-year = {2000}
-}
-@article{Heckman1976,
-abstract = {This paper presents a unified treatment of statistical models for truncation, sample selection and limited dependent variables. A simple estimator is proposed that permits estimation of those models by least squares, and probit analysts. In an empirical example, it is shown that the estimator yields estimates close to the maximum likelihood estimates.},
-author = {Heckman, James J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Heckman - 1976 - The common structure of statistical models of truncation, sample selection, and limited dependent variables and a simpl.pdf:pdf},
-journal = {Annals of Economic and Social Measurement},
-number = {4},
-pages = {475--492},
-title = {{The common structure of statistical models of truncation, sample selection, and limited dependent variables and a simple estimator for such models}},
-url = {http://econpapers.repec.org/bookchap/nbrnberch/10491.htm},
-volume = {5},
-year = {1976}
-}
-@article{Ricklefs2004,
-abstract = {The present study proposes to reconcile the different spatial and temporal scales of regional species production and local constraint on species richness. Although interactions between populations rapidly achieve equilibrium and limit membership in ecological communities locally, these interactions occur over heterogeneous environments within large regions, where the populations of species are stably regulated through competition and habitat selection. Consequently, exclusion of species from a region depends on long-term regional-scale environmental change or evolutionary change among interacting populations, bringing species production and extinction onto the same scale and establishing a link between local and regional processes.},
-author = {Ricklefs, Robert E.},
-doi = {10.1046/j.1461-0248.2003.00554.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricklefs - 2004 - A comprehensive framework for global patterns in biodiversity.pdf:pdf},
-journal = {Ecology Letters},
-number = {1},
-pages = {1--15},
-title = {{A comprehensive framework for global patterns in biodiversity}},
-volume = {7},
-year = {2004}
-}
-@article{Milanovic1997,
-abstract = {The paper proposes a new, and a much simpler, way to calculate the Gini coefficient. The existence of a relationship between linear (concave or convex) Pen's income parade, and specific values of the Gini coefficient is derived.},
-author = {Milanovic, Branco},
-doi = {10.1016/S0165-1765(97)00101-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Milanovic - 1997 - A simple way to calculate the Gini coefficient and some applications.pdf:pdf},
-journal = {Economics Letters},
-number = {1},
-pages = {45--49},
-title = {{A simple way to calculate the Gini coefficient and some applications}},
-url = {http://www.sciencedirect.com/science/article/pii/S0165176597001018},
-volume = {56},
-year = {1997}
-}
-@book{Magurran2004,
-address = {Oxford},
-author = {Magurran, Anne E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Magurran - 2004 - Measuring Biological Diversity.pdf:pdf},
-isbn = {978-1-118-68792-5},
-publisher = {Blackwell Publishing},
-title = {{Measuring Biological Diversity}},
-year = {2004}
-}
-@article{Izsak2012,
-abstract = {Species abundance distribution (SAD) is a classic topic of multispecies ecology. Different types of SAD may indicate specific environmental conditions. A possible way to present some properties of a theoretical or empirical SAD is the construction of a rank-abundance curve (RAC). With regard to the applicability of the RAC as a widely used indicator of the structure of a multispecies community and of the ecological status of its habitat, a basic question is the link between the type of SAD and the shape of the associated RAC. One of the simplest ways to characterize a RAC is to determine its concave and convex segments. However, none of ecological textbooks does give a clear-cut guideline concerning this issue. In the paper a connection is presented between some types of SAD and the convex and concave segments of the related RAC: including among others linearity for the geometric SAD (e.g. with communities in early stage of succession), convexity for the Zipf{\^{a}}€“Mandelbrot SAD (e.g. with communities with slow successional process), and convexity and then concavity with an inflexion point at approximately the mode of the associated histogram for the lognormal SAD (e.g. with climax, equilibrium communities). Our approach has the potential to improve and justify the use of RACs when searching for the determinants of community structure, initiating further studies in this field.},
-annote = {doi: 10.1016/j.ecolind.2011.06.030},
-author = {Izs{\'{a}}k, J{\'{a}}nos and Pavoine, Sandrine},
-doi = {10.1016/j.ecolind.2011.06.030},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Izs{\'{a}}k, Pavoine - 2012 - Links between the species abundance distribution and the shape of the corresponding rank abundance curve.pdf:pdf},
-journal = {Ecological Indicators},
-number = {1},
-pages = {1--6},
-title = {{Links between the species abundance distribution and the shape of the corresponding rank abundance curve}},
-url = {http://www.sciencedirect.com/science/article/pii/S1470160X11002019},
-volume = {14},
-year = {2012}
-}
-@article{GarciaMartin2006,
-abstract = {We present an explanation for the widely reported power-law species{\^{a}}€“area relationship (SAR), which relates the area occupied by a biome to the number of species that it supports. We argue that power-law SARs are a robust consequence of a skewed species abundance distribution resembling a lognormal with higher rarity, together with the observation that individuals of a given species tend to cluster. We show that the precise form of the SAR transcends the specific details of organism interactions, enabling us to characterize its broad trends across taxa.},
-author = {{G{\'{a}}rcia Mart{\'{i}}n}, H{\'{e}}ctor and Goldenfeld, Nigel},
-doi = {10.1073/pnas.0510605103},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/G{\'{a}}rcia Mart{\'{i}}n, Goldenfeld - 2006 - On the origin and robustness of power-law species-area relationships in ecology.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {27},
-pages = {10310--10315},
-title = {{On the origin and robustness of power-law species-area relationships in ecology}},
-url = {http://www.pnas.org/content/103/27/10310.abstract},
-volume = {103},
-year = {2006}
-}
-@article{Bennett1985,
-abstract = {This paper examines, by example, approaches to the statistical analysis of spatial structure and spatial interaction in geography. Both static and dynamic models are discussed with an emphasis on models that derive from geographical theory. Two themes are emphasized and developed: first, the need to accommodate mutual dependencies between elements of structure and interaction flows; second, for dynamic analysis, the need to take explicit account of the speed (“fast”/“slow”) with which the elements of any spatial system adjust. The paper concludes with a discussion of research problems.},
-author = {Bennett, R. J. and Haining, R. P.},
-doi = {10.2307/2981508},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bennett, Haining - 1985 - Spatial Structure and Spatial Interaction Modelling Approaches to the Statistical Analysis of Geographical Dat.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {1},
-pages = {1--36},
-title = {{Spatial Structure and Spatial Interaction: Modelling Approaches to the Statistical Analysis of Geographical Data}},
-url = {https://www.jstor.org/stable/2981508},
-volume = {148},
-year = {1985}
-}
-@article{Pereira2013,
-abstract = {Reducing the rate of biodiversity loss and averting dangerous biodiversity change are international goals, reasserted by the Aichi Targets for 2020 by Parties to the United Nations (UN) Convention on Biological Diversity (CBD) after failure to meet the 2010 target. However, there is no global, harmonized observation system for delivering regular, timely data on biodiversity change. With the first plenary meeting of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) soon under way, partners from the Group on Earth Observations Biodiversity Observation Network (GEO BON) are developing—and seeking consensus around—Essential Biodiversity Variables (EBVs) that could form the basis of monitoring programs worldwide.},
-author = {Pereira, H. M. and Ferrier, Simon and Walters, M. and Geller, G. N. and Jongman, R. H. G. and Scholes, R. J. and Bruford, M. W. and Brummitt, N. and Butchart, S. H. M. and Cardoso, A. C. and Coops, N. C. and Dulloo, E. and Faith, Daniel P. and Freyhof, J. and Gregory, R. D. and Heip, C. and H{\"{o}}ft, R. and Hurtt, G. and Jetz, W. and Karp, D. S. and McGeoch, M. A. and Obura, D. and Onoda, Y. and Pettorelli, N. and Reyers, B. and Sayre, R. and Scharlemann, J. P. W. and Stuart, S. N. and Turak, E. and Walpole, M. and Wegmann, M.},
-doi = {10.1126/science.1229931},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pereira et al. - 2013 - Essential biodiversity variables.pdf:pdf},
-journal = {Science},
-pages = {277--278},
-title = {{Essential biodiversity variables}},
-url = {http://science.sciencemag.org/content/339/6117/277},
-volume = {339},
-year = {2013}
-}
-@article{Mion2004,
-abstract = {This paper aims at assessing the role of market linkages in shaping the spatial distribution of earnings. Using a space-time panel data on Italian provinces, I structurally estimate a NEG model in order to both test the coherence of theory with data, as well as to give a measure of the extent of spatial externalities. Particular attention has been paid to those endogeneity issues that arise when dealing with both structural models and spatial data. Results suggest that final demand linkages influence the location of economic activities and that their spread over space is, contrary to previous findings, not negligible.},
-author = {Mion, Giordano},
-doi = {10.1016/j.jue.2004.03.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mion - 2004 - Spatial externalities and empirical analysis the case of Italy.pdf:pdf},
-journal = {Journal of Urban Economics},
-pages = {97--118},
-title = {{Spatial externalities and empirical analysis: the case of Italy}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119004000348},
-volume = {56},
-year = {2004}
-}
-@article{Baselga2010a,
-author = {Baselga, Andr{\'{e}}s},
-doi = {doi:10.1890/09-0320.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baselga - 2010 - Multiplicative partition of true diversity yields independent alpha and beta components additive partition does not.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1974--1981},
-title = {{Multiplicative partition of true diversity yields independent alpha and beta components; additive partition does not}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-0320.1},
-volume = {91},
-year = {2010}
-}
-@article{Asner2014,
-abstract = {Patterns of tropical forest functional diversity express processes of ecological assembly at multiple geographic scales and aid in predicting ecological responses to environmental change. Tree canopy chemistry underpins forest functional diversity, but the interactive role of phylogeny and environment in determining the chemical traits of tropical trees is poorly known. Collecting and analyzing foliage in 2,420 canopy tree species across 19 forests in the western Amazon, we discovered (i) systematic, community-scale shifts in average canopy chemical traits along gradients of elevation and soil fertility; (ii) strong phylogenetic partitioning of structural and defense chemicals within communities independent of variation in environmental conditions; and (iii) strong environmental control on foliar phosphorus and calcium, the two rock-derived elements limiting CO2 uptake in tropical forests. These findings indicate that the chemical diversity of western Amazonian forests occurs in a regionally nested mosaic driven by long-term chemical trait adjustment of communities to large-scale environmental filters, particularly soils and climate, and is supported by phylogenetic divergence of traits essential to foliar survival under varying environmental conditions. Geographically nested patterns of forest canopy chemical traits will play a role in determining the response and functional rearrangement of western Amazonian ecosystems to changing land use and climate.},
-author = {Asner, Gregory P. and Martin, Roberta E. and Tupayachi, Raul and Anderson, Christopher B. and Sinca, Felipe and Carranza-Jim{\'{e}}nez, Loreli and Martinez, Paola},
-doi = {10.1073/pnas.1401181111},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Asner et al. - 2014 - Amazonian functional diversity from forest canopy chemical assembly.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {15},
-pages = {5604--5609},
-title = {{Amazonian functional diversity from forest canopy chemical assembly}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3992634{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {111},
-year = {2014}
-}
-@article{Jost2010a,
-author = {Jost, Lou},
-doi = {10.1890/09-0368.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2010 - Independence of alpha and beta diversities.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1969--1994},
-title = {{Independence of alpha and beta diversities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/09-0368.1/abstract},
-volume = {91},
-year = {2010}
-}
-@article{Dauby2012,
-abstract = {A theoretical framework based on Hill numbers has recently been advocated to measure and partition diversity sensu stricto. Hill numbers can be interpreted intuitively as effective number of species (ENS). They conform to the so-called replication principle allowing a mathematically coherent multiplicative partitioning of diversity. They form a family of ENS defined by the parameter q which controls the weight attributed to rare species. Despite its advantages, this framework was developed without considering its robustness when treating community samples. In this study, we first show that Hurlbert diversity indices (expected number of species among k individuals) can be transformed into ENS that conform asymptotically to the replication principle while controlling the weight given to rare species through parameter k. We investigate the statistical properties of Hill and Hurlbert ENS using simulated communities with contrasted diversity. The properties of multiplicative beta diversity estimators based on ENS are also characterized by simulating communities with different levels of differentiation. We show that Hurlbert ENS provides a better statistical performance than Hill numbers when dealing with small sample sizes. By contrast, Hill numbers and their estimators suffer from substantial bias except when rare species have a low weight (q= 2). An estimator of ENS estimating both Hill numbers for q= 2 and Hurlbert ENS for k= 2 is shown to give the best performance and is recommended for processing real datasets when rare species receive low weight. In order to better take account of rare species, current estimators of Hill numbers are not recommended when sample size is too low while Hurlbert's ENS performs reliably. In conclusion, while Hill numbers possess some interesting mathematical properties that are not shared by Hurlbert's ENS, the latter outperforms Hill numbers in terms of statistical properties and is well suited to processing community samples, as illustrated on a real dataset. {\textcopyright} 2011 The Authors. Ecography {\textcopyright} 2011 Nordic Society Oikos.},
-annote = {Export Date: 19 October 2012
-Source: Scopus
-CODEN: ECOGE
-Language of Original Document: English
-Correspondence Address: Dauby, G.; Evolutionary Biology and Ecology unit, Univ. Libre de Bruxelles, Facult{\'{e}} des Sciences, CP 160/12, Av. F.D. Roosevelt, 50, BE-1050 Brussels, Belgium; email: gildauby@gmail.com},
-author = {Dauby, Gilles and Hardy, Olivier J.},
-doi = {10.1111/j.1600-0587.2011.06860.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dauby, Hardy - 2012 - Sampled-based estimation of diversity sensu stricto by transforming Hurlbert diversities into effective number of.pdf:pdf},
-journal = {Ecography},
-number = {7},
-pages = {661--672},
-title = {{Sampled-based estimation of diversity sensu stricto by transforming Hurlbert diversities into effective number of species}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84862766998{\&}partnerID=40{\&}md5=4ba29a45424456ea1b2ed026306de7ba},
-volume = {35},
-year = {2012}
-}
-@article{Oddou-Muratorio2004,
-abstract = {Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in approximately 100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.},
-annote = {Kcor},
-author = {Oddou-Muratorio, Sylvie and Demesure-Musch, Brigitte and P{\'{e}}lissier, Rapha{\"{e}}l and Gouyon, Pierre-Henri},
-doi = {10.1111/j.1365-294X.2004.02373.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Oddou-Muratorio et al. - 2004 - Impacts of gene flow and logging history on the local genetic structure of a scattered tree species, Sor.pdf:pdf},
-journal = {Molecular ecology},
-number = {12},
-pages = {3689--702},
-title = {{Impacts of gene flow and logging history on the local genetic structure of a scattered tree species, Sorbus torminalis L. Crantz.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/15548283},
-volume = {13},
-year = {2004}
-}
-@article{Roscher2004,
-abstract = {The focus of a new experiment, set up in Jena in spring 2002, are the effects of biodiversity on element cycles and the interaction of plant diversity with herbivores and soil fauna. The experimental design explicitly addresses criticisms provoked by previous biodiversity experiments. In particular, the choice of functional groups, the statistical separation of sampling versus complementarity effects, and testing for the effects of particular functional groups differ from previous experiments. Based on a species pool of 60 plant species common to the Central European Arrhenatherion grasslands, mixtures of one to 16 (60) species and of one to four plant functional groups were established on 90 plots (20 m × 20 m) with nested experiments. In order to test specific hypotheses 390 additional small-area plots (3.5m× 3.5 m) were set-up. Exact replicates of all species mixtures serve to assess the variability in ecosystem responses. In a dominance experiment, the effects of interactions among nine selected highly productive species are studied. Each species is grown as monoculture replicated once.},
-annote = {Article},
-author = {Roscher, Christiane and Schumacher, Jens and Baade, Jussi and Wilcke, Wolfgang and Gleixner, Gerd and Weisser, Wolfgang W. and Schmid, Bernhard and Schulze, Ernst-Detlef},
-doi = {10.1078/1439-1791-00216},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roscher et al. - 2004 - The role of biodiversity for element cycling and trophic interactions an experimental approach in a grassland co.pdf:pdf},
-journal = {Basic and Applied Ecology},
-number = {2},
-pages = {107--121},
-title = {{The role of biodiversity for element cycling and trophic interactions: an experimental approach in a grassland community}},
-url = {http://www.sciencedirect.com/science/article/pii/S1439179104701644},
-volume = {5},
-year = {2004}
-}
-@article{Weiner1995,
-author = {Weiner, Jacob},
-doi = {10.2307/2261159},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weiner - 1995 - On the practice of ecology.pdf:pdf},
-journal = {Journal of Ecology},
-pages = {153--158},
-title = {{On the practice of ecology}},
-url = {http://www.jstor.org/stable/2261159},
-volume = {83},
-year = {1995}
-}
-@article{Hirschman1964,
-author = {Hirschman, Albert O.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hirschman - 1964 - The Paternity of an Index.pdf:pdf},
-journal = {The American Economic Review},
-number = {5},
-pages = {761--762},
-title = {{The Paternity of an Index}},
-url = {http://www.jstor.org/stable/1818582},
-volume = {54},
-year = {1964}
-}
-@article{Ricotta2006a,
-abstract = {This reply paper includes two brief remarks in rejoinder to the commentary papers of Myers and Patil, Podani, and Sarkar. The first observation concerns the fundamental nature of ecological diversity measures, while the second one specifically addresses some interesting mathematical connections between $\alpha$- and $\beta$-diversity. {\textcopyright} 2006 Springer Science + Business Media, Inc.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: ABIOA
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1007/s10441-006-8258-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2006 - Towards a complex, plural and dynamic approach to diversity Rejoinder to Myers and Patil, Podani, and Sarkar.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {2},
-pages = {141--146},
-title = {{Towards a complex, plural and dynamic approach to diversity: Rejoinder to Myers and Patil, Podani, and Sarkar}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33748976341{\&}partnerID=40{\&}md5=f97ef02326fce7f3834a6b26597b26d1},
-volume = {54},
-year = {2006}
-}
-@phdthesis{Pavoine2005b,
-author = {Pavoine, Sandrine},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine - 2005 - Mod{\`{e}}les statistisques pour la mesure de la biodiversit{\'{e}}.pdf:pdf},
-pages = {413},
-publisher = {Universit{\'{e}} Claude Bernard, Lyon I},
-title = {{Mod{\`{e}}les statistisques pour la mesure de la biodiversit{\'{e}}}},
-url = {http://pbil.univ-lyon1.fr/R/pdf/these{\_}sp.pdf},
-year = {2005}
-}
-@article{Balaguer2001,
-abstract = {1, Quercus coccifera, a slow-growing, evergreen oak, grows in contrasting environments in the Mediterranean Basin. Habitat-based selection may have promoted divergence between populations with respect to phenotypic plasticity and genetic variability. 2. We tested the hypothesis that populations of the Q, coccifera originating from a rock outcrop, a continental garrigue formation and an oceanic forest would differ in their plastic response to light intensity. Plants from these populations were grown from acorns in a common garden at 100{\%} and 20{\%} full sunlight. Light response analysis was based on photochemical efficiency, xanthophyll pool, nutrient allocation, growth, crown architecture and light absorption. 3, Light-responsive characters ranged from the subcellular to the whole-plant level. The greatest divergences between sun and shade phenotypes were observed in leaf size, leaf angle and leaf area ratio. However, plasticity in these traits depended on plant provenance. 4, Regardless of the level of organization, populations were invariably ranked in the same order of plasticity when averaged over light-responsive features, with plants originating from the rock outcrop showing the least plasticity and those from the forest the largest. The forest population also had the greatest genetic variability with respect to the isoperoxidase polymorphism. 5, Among populations, plants originating from the phosphorus-deficient rock outcrop contained 30{\%} more P per unit dry weight. Plants from the forest population had 5{\%} more photoprotective xanthophylls, 30{\%} larger total leaf area, with less lobed and larger leaves and a differential plasticity in leaf azimuth. 6, Differences among populations suggested ecotypic differentiation towards less phenotypic plasticity in the most homogeneous light environments. The ecological breadth of the species seemed to be derived not only from its tolerance of Mediterranean conditions but also from the specialization of its populations in contrasting habitats.},
-author = {Balaguer, L. and Martinez-Ferri, E. and Valladares, F. and Perez-Corona, M. E. and Baquedano, F. J. and Castillo, F. J. and Manrique, E.},
-doi = {10.1046/j.1365-2435.2001.00505.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Balaguer et al. - 2001 - Population divergence in the plasticity of the response of Quercus coccifera to the light environment.pdf:pdf},
-journal = {Functional Ecology},
-number = {1},
-pages = {124--135},
-title = {{Population divergence in the plasticity of the response of Quercus coccifera to the light environment}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2435.2001.00505.x/full},
-volume = {15},
-year = {2001}
-}
-@article{Umana2017,
-abstract = {Trait-based studies in community ecology have generally focused on the community as a unit where all species occur due to stochasticity, determinism or some mixture of the two. However, the processes governing population dynamics may vary greatly among species. We propose a core-transient framework for trait-based community studies where a core group of species has a strong link to the local environment while transient species have weaker responses to the environment. Consistent with the expectations of the framework, we found that common species exhibit clear linkages between performance and their environment and traits while rare species tend to have weaker or non-significant relationships. Ultimately, trait-based ecology should move beyond applying a set of processes to a community as a whole and towards quantifying inter-specific variation in the drivers of population dynamics that ultimately scale up to determine community structure.},
-author = {Uma{\~{n}}a, Maria Natalia and Zhang, Caicai and Cao, Min and Lin, Luxiang and Swenson, Nathan G.},
-doi = {10.1111/ele.12760},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Uma{\~{n}}a et al. - 2017 - A core-transient framework for trait-based community ecology an example from a tropical tree seedling community.pdf:pdf},
-journal = {Ecology Letters},
-number = {5},
-pages = {619--628},
-title = {{A core-transient framework for trait-based community ecology: an example from a tropical tree seedling community}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12760/abstract},
-volume = {20},
-year = {2017}
-}
-@article{Lamb2009,
-abstract = {Statistically rigorous methods for summarizing and reporting trends in the intactness of biodiversity are a key element of effective biodiversity monitoring programs. There are four major approaches for translating complex monitoring data into easily communicated summary statistics: (1) traditional diversity indices such as species richness and Simpson's diversity, (2) species intactness indices based on occurrence, (3) species intactness indices based on abundance, and (4) multivariate community indices. We use simulated data to evaluate the effectiveness of 13 indices from these four categories based on statistical robustness, sensitivity to errors and noise in the data, ecological relevance, and ease of communication. We show that indices that calculate species intactness using equations like Buckland's arithmetic mean index are the most effective for use in large-scale biodiversity intactness monitoring programs. Traditional diversity indices are unsuitable for monitoring of biodiversity intactness, and multivariate indices can be highly sensitive to errors and noise in the data. Finally, we provide guidelines for the application of these indices in biodiversity intactness monitoring.},
-author = {Lamb, Eric G. and Bayne, Erin and Holloway, Gillian and Schieck, Jim and Boutin, Stan and Herbers, Jim and Haughland, Diane L.},
-doi = {10.1016/j.ecolind.2008.06.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lamb et al. - 2009 - Indices for monitoring biodiversity change Are some more effective than others.pdf:pdf},
-journal = {Ecological Indicators},
-number = {3},
-pages = {432--444},
-title = {{Indices for monitoring biodiversity change: Are some more effective than others?}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X08000733},
-volume = {9},
-year = {2009}
-}
-@article{DeGroot2002,
-abstract = {An increasing amount of information is being collected on the ecological and socio-economic value of goods and services provided by natural and semi-natural ecosystems. However, much of this information appears scattered throughout a disciplinary academic literature, unpublished government agency reports, and across the World Wide Web. In addition, data on ecosystem goods and services often appears at incompatible scales of analysis and is classified differently by different authors. In order to make comparative ecological economic analysis possible, a standardized framework for the comprehensive assessment of ecosystem functions, goods and services is needed. In response to this challenge, this paper presents a conceptual framework and typology for describing, classifying and valuing ecosystem functions, goods and services in a clear and consistent manner. In the following analysis, a classification is given for the fullest possible range of 23 ecosystem functions that provide a much larger number of goods and services. In the second part of the paper, a checklist and matrix is provided, linking these ecosystem functions to the main ecological, socio–cultural and economic valuation methods.},
-author = {de Groot, Rudolf S. and Wilson, Matthew A. and Boumans, Roelof M. J.},
-doi = {10.1016/S0921-8009(02)00089-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Groot, Wilson, Boumans - 2002 - A typology for the classification, description and valuation of ecosystem functions, goods and servic.pdf:pdf},
-journal = {Ecological Economics},
-number = {3},
-pages = {393--408},
-title = {{A typology for the classification, description and valuation of ecosystem functions, goods and services}},
-url = {http://www.sciencedirect.com/science/article/pii/S0921800902000897},
-volume = {41},
-year = {2002}
-}
-@techreport{Barrios2003,
-abstract = {We investigate and compare the spatial distribution of manufacturing activity and its determinants in Belgium, Ireland and Portugal using comparable, exhaustive micro-level data sets. We find some similarities between Portugal and Belgium, but little for Ireland. Moreover, there is some evidence that forward and backward linkages as well as dependence on natural avantages can be important determinants of agglomeration.},
-author = {Barrios, Salvador and Bertinelli, Luisito and Strobl, Eric and Teixeira, Antonio Carlos Fernandes},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barrios et al. - 2009 - Spatial Distribution of Manufacturing Activity and its Determinants A Comparison of Three Small European Countri.pdf:pdf},
-isbn = {2003/67},
-title = {{Agglomeration economies and the location of industries: a comparison of three small European countries}},
-url = {https://papers.ssrn.com/sol3/papers.cfm?abstract{\_}id=989928},
-year = {2003}
-}
-@article{Tilman1994a,
-author = {Tilman, D.},
-doi = {10.1126/science.283.5401.495},
-issn = {00368075},
-journal = {Science},
-month = {jan},
-number = {5401},
-pages = {495--496},
-title = {{Diversity by Default}},
-url = {http://www.sciencemag.org/cgi/doi/10.1126/science.283.5401.495},
-volume = {283},
-year = {1994}
-}
-@article{Breheny2013,
-abstract = {Regression models allow one to isolate the relationship between the outcome and an ex planatory variable while the other variables are held constant. Here, we introduce an R package, visreg, for the convenient visualization of this relationship via short, simple function calls. In addition to estimates of this relationship, the package also provides pointwise confidence bands and partial residuals to allow assessment of variability as well as outliers and other deviations from modeling assumptions. The package provides several options for visualizing models with interactions, including lattice plots, contour plots, and both static and interactive perspective plots. The implementation of the package is designed to be fully object-oriented and interface seamlessly with R's rich collection of model classes, allowing a consistent interface for visualizing not only linear models, but generalized linear models, proportional hazards models, generalized additive models, robust regression models, and many more.},
-author = {Breheny, Patrick and Burchett, Woodrow},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Breheny, Burchett - 2013 - Visualization of regression models using visreg.pdf:pdf},
-journal = {R package},
-number = {2},
-pages = {56--71},
-title = {{Visualization of regression models using visreg}},
-url = {http://cran.r-project.org/package=visreg},
-volume = {9},
-year = {2013}
-}
-@article{Lonsdale1999,
-abstract = {With a simple model, I show that comparisons of invasibility between regions are impossible to make unless one can control for all of the variables besides invasibility that influence exotic richness, including the rates of immigration of species and the characteristics of the invading species themselves. Using data from the literature for 184 sites around the world, I found that nature reserves had one-half of the exotic fraction of sites outside reserves, and island sites had nearly three times the exotic fraction of mainland sites. However, the exotic fraction and the number of exotics were also dependent on site area, and this had to be taken into account to make valid comparisons between sites. The number of native species was used as a surrogate for site area and habitat diversity. Nearly 70{\%} of the variation in the number of exotic species was accounted for by a multiple regression containing the following predictors: the number of native species, whether the site was an island or on the mainland, and whether or not it was a nature reserve. After controlling for scale, there were significant differences among biomes, but not continents, in their level of invasion. Multiple biome regions and temperate agricultural or urban sites were among the most invaded biomes, and deserts and savannas were among the least. However, there was considerable within-group variation in the mean degree of invasion. Scale-controlled analysis also showed that the New World is significantly more invaded than the Old World, but only when site native richness (probably a surrogate for habitat diversity) is factored out. Contrary to expectation, communities richer in native species had more, not fewer, exotics. For mainland sites, the degree of invasion increased with latitude, but there was no such relationship for islands. Although islands are more invaded than mainland sites, this is apparently not because of low native species richness, as the islands in this data set were no less rich in native species than were mainland sites of similar area. The number of exotic species in nature reserves increases with the number of visitors. However, it is difficult to draw conclusions about relative invasibility, invasion potential, or the roles of dispersal and disturbance from any of these results. Most of the observed patterns here and in the literature could potentially be explained by differences between regions in species properties, ecosystem properties, or propagule pressure.},
-annote = {ArticleType: research-article / Full publication date: Jul., 1999 / Copyright {\^{A}}{\textcopyright} 1999 Ecological Society of America},
-author = {Lonsdale, W. M.},
-doi = {10.2307/176544},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lonsdale - 1999 - Global Patterns of Plant Invasions and the Concept of Invasibility.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1522--1536},
-title = {{Global Patterns of Plant Invasions and the Concept of Invasibility}},
-url = {http://www.jstor.org/stable/176544},
-volume = {80},
-year = {1999}
-}
-@article{Hoel1943,
-author = {Hoel, Paul G.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hoel - 1943 - On Indices of Dispersion.pdf:pdf},
-journal = {The Annals of Mathematical Statistics},
-keywords = {Hoel (1943).pdf},
-mendeley-tags = {Hoel (1943).pdf},
-number = {2},
-pages = {155--162},
-title = {{On Indices of Dispersion}},
-volume = {14},
-year = {1943}
-}
-@article{Bender1998,
-abstract = {We evaluated the conditions under which patch size effects are important determinants of local population density for animals living in patchy landscapes. This information was used to predict when patch size effects will be expected to occur following habitat loss and fragmentation. Using meta-analysis, we quantitatively reviewed the results of 25 published studies that tested for a relationship between patch size and population density. Patch size effects were strong for edge and interior species (negative and postive patch size effects, respectively), but negligible for generalist species that use both edge and interior habitat. We found significant differences in mean patch size effects between migratory and residential species, between herbivores and carnivores, and among taxonomic groups. We found no evidence that patch size effects were related to landscape characteristics such as the proportion of landscape covered by habitat, median patch size, or the scale at which a study was conducted. However, species in the Western Hemisphere tended to have larger absolute effect sizes, and eastern species tended to be more variable in their response. For landscapes undergoing habitat loss and fragmentation, our results predict the following: (1) among generalist species that use both the edge and the interior of a habitat patch, the decline in population size associated with habitat destruction should be accounted for by pure habitat loss alone; (2) for interior species, the decline in population size associated with habitat fragmentation per se will be greater than that predicted from pure habitat loss alone; (3) for edge species, the decline in population size will be less than that predicted by pure habitat loss alone; (4) these relative effects will not be influenced by the extent of habitat loss, but they will be affected by the pattern of habitat when large or small patches are preferentially removed; and (5) as loss and fragmentation increase within a landscape, migratory species will generally suffer less of a decline in population size than resident species.},
-author = {Bender, Darren J. and Contreras, Thomas A. and Fahrig, Lenore},
-doi = {10.1890/0012-9658(1998)079[0517:HLAPDA]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bender, Contreras, Fahrig - 1998 - Habitat loss and population decline A meta-analysis of the patch size effect.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {517--533},
-title = {{Habitat loss and population decline: A meta-analysis of the patch size effect}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(1998)079[0517:HLAPDA]2.0.CO;2/abstract},
-volume = {79},
-year = {1998}
-}
-@article{Chao2004a,
-abstract = {The classic Jaccard and S{\o}rensen indices of compositional similarity (and other indices that depend upon the same variables) are notoriously sensitive to sample size, especially for assemblages with numerous rare species. Further, because these indices are based solely on presence–absence data, accurate estimators for them are unattainable. We provide a probabilistic derivation for the classic, incidence-based forms of these indices and extend this approach to formulate new Jaccard-type or S{\o}rensen-type indices based on species abundance data. We then propose estimators for these indices that include the effect of unseen shared species, based on either (replicated) incidence- or abundance- based sample data. In sampling simulations, these new estimators prove to be considerably less biased than classic indices when a substantial proportion of species are missing from samples. Based on species-rich empirical datasets, we show how incorporating the effect of unseen shared species not only increases accuracy but also can change the interpretation of results. Keywords},
-author = {Chao, Anne and Chazdon, Robin L. and Colwell, Robert K. and Shen, Tsung-Jen},
-doi = {10.1111/j.1461-0248.2004.00707.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2004 - A new statistical approach for assessing similarity of species composition with incidence and abundance data.pdf:pdf},
-journal = {Ecology Letters},
-number = {2},
-pages = {148--159},
-title = {{A new statistical approach for assessing similarity of species composition with incidence and abundance data}},
-url = {http://doi.wiley.com/10.1111/j.1461-0248.2004.00707.x},
-volume = {8},
-year = {2004}
-}
-@article{Pielou1959,
-abstract = {1. The most straightforward method of assessing the degree of non-randomness, if any, of a plant population is to collect a sample of distances from random points to the plant individuals nearest them. A knowledge of the density of the individuals, independently determined, is also necessary. 2. An an index of non-randomness a = $\pi$ D$\omega$ is suggested, where D is density and $\omega$ is the mean of the squares of the point-to-plant distances. a is equal to, less than or greater than (n - 1)/n according as the population is random, regular or aggregated. The significance of a departure of a from this value is easily found since 2na is distributed like $\chi$2 with 2n degrees of freedom. Observed values of a from two non-random populations may be compared by a t-test. 3. The advantage of using this index is that it will reveal all the non-randomness present and not merely the smallest scale of non-randomness as an index based on plant-to-plant distances would. Also no distances need be measured from randomly chosen plants; the selection of truly random plants is exceedingly laborious and a biased sample is useless as it is likely to give most misleading results. 4. Owing to the fact that point-to-plant distances may sometimes have the same frequency distribution in random, regular or aggregated populations, the observed distribution of this variate will not necessarily, by itself, reveal non-randomness. The writer is at present investigating the distribution of point-to-plant distances in regular populations.},
-author = {Pielou, Evelyn C.},
-doi = {10.2307/2257293},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1959 - The Use of Point-to-Plant Distances in the Study of the Pattern of Plant Populations.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {607--613},
-title = {{The Use of Point-to-Plant Distances in the Study of the Pattern of Plant Populations}},
-url = {https://www.jstor.org/stable/2257293},
-volume = {47},
-year = {1959}
-}
-@article{Legendre2005,
-abstract = {Robert H. Whittaker defined beta diversity as the variation in species composition among sites in a geographic area. Beta diversity is a key concept for understanding the functioning of ecosystems, for the conservation of biodiversity, and for ecosystem management. This paper explains how hypotheses about the origin of beta diversity can be tested by partitioning the spatial variation of community composition data (presence– absence or abundance data) with respect to environmental variables and spatial base functions. We compare two statistical methods to accomplish that. The sum-of-squares of a community composition data table, which is one possible measure of beta diversity, is correctly partitioned by canonical ordination; hence, canonical partitioning produces correct estimates of the different portions of community composition variation. In recent years, several authors interested in the variation in community composition among sites (beta diversity) have used another method, variation partitioning on distance matrices (Mantel approach). Their results led us to compare the two partitioning approaches, using simulated data generated under hypotheses about the variation of community composition among sites. The theoretical developments and simulation results led to the following observations: (1) the variance of a community composition table is a measure of beta diversity. (2) The variance of a dissimilarity matrix among sites is not the variance of the community composition table nor a measure of beta diversity; hence, partitioning on distance matrices should not be used to study the variation in community composition among sites. (3) In all of our simulations, partitioning on distance matrices underestimated the amount of variation in community composition explained by the raw-data approach, and (4) the tests of significance had less power than the tests of canonical ordination. Hence, the proper statistical procedure for partitioning the spatial variation of community composition data among environmental and spatial components, and for testing hypotheses about the origin and maintenance of variation in community composition among sites, is canonical partitioning. The Mantel approach is appropriate for testing other hypotheses, such as the variation in beta diversity among groups of sites. Regression on distance matrices is also appropriate for fitting models to similarity decay plots.},
-author = {Legendre, Pierre and Borcard, Daniel and Peres-Neto, Pedro R},
-doi = {10.1890/05-0549},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Borcard, Peres-Neto - 2005 - Analyzing Beta Diversity Partitioning the Spatial Variation of Community Composition Data.pdf:pdf},
-journal = {Ecological Monographs},
-number = {4},
-pages = {435--450},
-title = {{Analyzing Beta Diversity: Partitioning the Spatial Variation of Community Composition Data}},
-url = {http://dx.doi.org/10.1890/05-0549},
-volume = {75},
-year = {2005}
-}
-@article{Kuuluvainen2000,
-abstract = {Understorey regeneration was studied on two sites with different fire histories in a 4 ha plot of mature Pinus sylvestris forest in the Petkeljarvi National Park in eastern Finland. The plot was divided based on fire history. In one part the last fire was a stand-replacing fire in the early 19th century, after which the whole stand regenerated; the remaining plot area was subsequently burnt by a surface fire in 1906. Understorey P. sylvestris individuals were more abundant in the area of the 1906 burn than in the area of the oldest burn. In both areas the size frequency distribution of living trees was bimodal, with frequency peaks at {\textless}5 cm and 30-150 cm height classes. In the older burnt area small understorey trees occurred on microsites created by tree fall disturbances, while in the 1906 burn area most small understorey trees occurred on vegetation-covered microsites. This indicates that with increasing time since last fire establishment of new understorey trees becomes more restricted by the availability of microsites created by tree fall disturbances. In both areas the proportion of vigorous small understorey trees was highest on decayed wood. In the older burnt area uprooted pits and mounds also has a significant proportion of small healthy understorey trees. The majority of trees classified as weak or dying were growing on microhabitats characterised by undisturbed vegetation. Ripley's K-function analyses showed that spatial distribution of understorey trees was clustered in both areas in all microsite types and clustering at small scales was most pronounced in understorey trees growing in uprooted spots or in association with decaying wood. The bivariate analysis showed a significant repulsion effect between large trees and understorey trees at intermediate spatial scales, indicating that competition had an effect on understorey tree distribution. This effect was more pronounced in the younger burnt area. It is concluded that in Pinus sylvestris forests the abundance, quality and spatial pattern of understorey tree population may vary considerably as a function of disturbance history.},
-author = {Kuuluvainen, Timo and Rouvinen, Seppo},
-doi = {10.2307/3236550},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kuuluvainen, Rouvinen - 2000 - Post-fire understorey regeneration in boreal Pinus sylvestris forest sites with different fire histories.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {801--812},
-title = {{Post-fire understorey regeneration in boreal Pinus sylvestris forest sites with different fire histories}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236550/abstract},
-volume = {11},
-year = {2000}
-}
-@article{Spellerberg2003,
-abstract = {In the literature, the terms species richness and species diversity are sometimes used interchangeably. We suggest that at the very least, authors should define what they mean by either term. Of the many species diversity indices used in the literature, the Shannon Index is perhaps most commonly used. On some occasions it is called the Shannon–Wiener Index and on other occasions it is called the Shannon–Weaver Index. We suggest an explanation for this dual use of terms and in so doing we offer a tribute to the late Claude Shannon (who passed away on 24 February 2001).},
-author = {Spellerberg, Ian F. and Feder, Peter J.},
-doi = {10.1046/j.1466-822X.2003.00015.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Spellerberg, Feder - 2003 - A tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species divers.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {3},
-pages = {177--179},
-title = {{A tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon–Wiener' Index}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1466-822X.2003.00015.x/abstract},
-volume = {12},
-year = {2003}
-}
-@book{Tomppo1986,
-address = {Helsinki, Finland},
-author = {Tomppo, E.},
-booktitle = {Communicationes Instituti Forestalis Fenniae},
-pages = {1--65},
-publisher = {The Finnish forest research institute},
-title = {{Models and methods for analysing spatial patterns of trees}},
-volume = {138},
-year = {1986}
-}
-@article{Tothmeresz1995,
-abstract = {The measurement of diversity, one of the most important concepts in present-day ecology, can be improved by methods of diversity ordering which have recently been developed. This ordering is achieved by a D($\alpha$) diversity index family. Indices of this family show varying sensitivities to the rare and abundant species as the scale parameter, $\alpha$, changes. The aim of this paper is to review and assess 12 methods of diversity ordering and discuss their relationships in detail. Two of the methods are new to the ecological literature. The diversity ordering methods are compared as to their effectiveness in graphically displaying the differences of community structure and demonstrating the (non-)comparability of communities. Small, medium and large data sets were used to evaluate the methods. A small artificial data set (five to seven species) and a large semi-artificial data set (31 — 141 species) are used in this paper. The results suggest that R{\'{e}}nyi's diversity index family and Logarithmic dominance ordering are the most useful methods for diversity ordering of communities of all sizes. Right-tailsum diversity ordering performs well for small communities.},
-annote = {Cited By (since 1996): 139
-Export Date: 8 November 2012
-Source: Scopus
-CODEN: JVESE
-Language of Original Document: English
-Correspondence Address: Tothmeresz, B.Hungary},
-author = {Tothmeresz, B{\'{e}}la},
-doi = {10.2307/3236223},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tothmeresz - 1995 - Comparison of different methods for diversity ordering.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {283--290},
-title = {{Comparison of different methods for diversity ordering}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236223/abstract},
-volume = {6},
-year = {1995}
-}
-@article{Chacon-Labella2016,
-abstract = {Abstract$\backslash$r$\backslash$n$\backslash$r$\backslash$nMost ecological theories that aim to explain coexistence in megadiverse communities employ a set of three rules to describe the stochastic geometry of biodiversity: (1) individuals exhibit intraspecific clustering; (2) species abundances vary according to a log-normal distribution; and (3) the spatial arrangement between species is independent. The first two rules have received strong empirical support, but the third remains largely unexplored.$\backslash$r$\backslash$nTo address this deficiency, we evaluated the independent species arrangement rule in a species-rich shrubland and its potential drivers, i.e., the levels of species richness and intraspecific clustering exhibited by a given species at different scales, and the relative abundance of such species in the community.$\backslash$r$\backslash$nWe found that interspecific associations were rare and that independence was positively related to species richness and intraspecific clustering, but negatively related to relative species abundances.$\backslash$r$\backslash$nSynthesis: Our results agree with the independent species arrangement rule and they provide empirical support for the stochastic geometry of biodiversity. In the context of species-rich plant communities, the likelihood of two species encountering is very small. However, our study demonstrated a novel feature of this context, where both intraspecific clustering (due limitations on dispersal) and relative species abundances play fundamental roles in determining the probability of two species encountering and interacting, especially at very fine spatial scales.},
-author = {Chac{\'{o}}n-Labella, Julia and de la Cruz, Marcelino and Escudero, Adri{\'{a}}n},
-doi = {10.1111/1365-2745.12710},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chac{\'{o}}n-Labella, de la Cruz, Escudero - 2017 - Evidence for a stochastic geometry of biodiversity the effects of species abundance, richn.pdf:pdf},
-journal = {Journal of Ecology},
-title = {{Evidence for a stochastic geometry of biodiversity: the effects of species abundance, richness and intraspecific clustering}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12710},
-volume = {in press},
-year = {2016}
-}
-@article{Ricotta2005a,
-abstract = {Question: According to Whittaker' s proposal, ecologists have traditionally viewed $\beta$-diversity as the ratio between $\gamma$-diversity and average $\alpha$-diversity. More recently, an alternative way of partitioning diversity has been 'rediscovered' for which $\beta$-diversity is obtained as the difference between $\gamma$-diversity and average $\alpha$-diversity. This additive way of partitioning diversity has rapidly become a very popular framework for hierarchical diversity decomposition at various spatial scales. The question for this study is: Can we highlight any relation between these two ways of partitioning diversity, or do these methods really capture different facets of spatial turnover in species composition? Methods: First the properties that a diversity measure should possess for enabling additive decomposition into $\alpha$-, $\beta$-, and $\gamma$-components are reviewed. Next, attention is drawn to the relationships between additive and multiplicative diversity decomposition. Results: It is shown that the additive model is closely related to its multiplicative counterpart through a simple logarithmic transformation. Conclusions: Contrary to the current assumption, both methods for partitioning diversity are not as different as they appear. Hence, the supposed superiority of additive diversity partition over multiplicative diversity decomposition is largely unjustified. {\textcopyright} IAVS; Opulus Press Uppsala.},
-annote = {Cited By (since 1996):17
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: JVESE
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; University of Rome 'La Sapienza', Department of Plant Biology, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniromal.it},
-author = {Ricotta, Carlo},
-doi = {10.1111/j.1654-1103.2005.tb02359.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2009 - On hierarchical diversity decomposition.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {223--226},
-title = {{On hierarchical diversity decomposition}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-20444435977{\&}partnerID=40{\&}md5=21891ba98a73f6a2e1c47d8edb4295b5},
-volume = {16},
-year = {2009}
-}
-@article{Nee2005,
-abstract = {Life-history theory attempts to provide evolutionary explanations for variations in the ways in which animal species live their lives. Recent analyses have suggested that the dimensionless ratios of several key life-history parameters are the same for different species, even across distant taxa. However, we show here that previous analyses may have given a false picture and created an illusion of invariants, which do not necessarily exist; essentially, this is because life-history variables have been regressed against themselves. The following question arises from our analysis: How do we identify an invariant?},
-author = {Nee, Sean and Colegrave, Nick and West, Stuart A. and Grafen, Alan},
-doi = {10.1126/science.1114488},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nee et al. - 2005 - The illusion of invariant quantities in life histories.pdf:pdf},
-journal = {Science},
-number = {5738},
-pages = {1236--1239},
-title = {{The illusion of invariant quantities in life histories}},
-volume = {309},
-year = {2005}
-}
-@article{Wright2001,
-abstract = {1. Relationships were examined among photosynthetic capacity (A(mass) and A(area)), foliar dark respiration rate (Rd-mass and Rd-area ), stomatal conductance to water (G(s)), specific leaf area (SLA), and leaf nitrogen (N) and phosphorus (P) across 79 perennial species occurring at four sites with contrasting rainfall levels and soil nutrients in eastern Australia. We hypothesized that the slope of log-log 'scaling' relationships between these traits would be positive and would not differ between sites, although slope elevations might shift between habitat types. 2. A(mass), Rd-mass SLA N-mass and P-mas, were positively associated in common slopes fitted across sites or rainfall zones, although rather weakly within individual sites in some cases. The relationships between A(mass) (and Rd-mass) with each of N-mass and SLA were partially independent of each other, with A(mass) (or Rd-mass) increasing with SLA at a given N-mass or with N as, at a given SLA (only weakly in the case of A(mass)). These results improve the quantification and extend the generalization of reported patterns to floras largely unlike those studied previously, with the additional contribution of including phosphorus data. 3. Species from drier sites differed in several important respects. They had (i) higher leaf N and P (per dry mass or area); (ii) lower photosynthetic capacity at a given leaf N or P; (iii) higher Rd-mass at a given SLA or A(mass); and (iv) lower G(s) at a given A(area) (implying lower internal CO2 concentration). 4. These trends can be interpreted as part of a previously undocumented water conservation strategy in species from dry habitats. By investing heavily in photosynthetic enzymes, a larger drawdown of internal CO2 concentration is achieved, and a given photosynthetic rate is possible at a lower stomatal conductance. Transpirational water use is similar, however, due to the lower-humidity air in dry sites. The benefit of the strategy is that dry-site species reduce water loss at a given A(area), down to levels similar to wet-site species, despite occurring in lower-humidity environments. The cost of high leaf N is reflected in higher dark respiration rates and, presumably, additional costs incurred by N acquisition and increased herbivory risk.},
-author = {Wright, Ian J. and Reich, Peter B. and Westoby, Mark},
-doi = {10.1046/j.0269-8463.2001.00542.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright, Reich, Westoby - 2001 - Strategy shifts in leaf physiology, structure and nutrient content between species of high- and low-rain.pdf:pdf},
-journal = {Functional Ecology},
-number = {4},
-pages = {423--434},
-title = {{Strategy shifts in leaf physiology, structure and nutrient content between species of high- and low-rainfall and high- and low-nutrient habitats}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.0269-8463.2001.00542.x/abstract},
-volume = {15},
-year = {2001}
-}
-@book{Magurran2011,
-address = {New York},
-author = {Magurran, Anne E. and McGill, Brian J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Magurran, McGill - 2011 - Biological diversity frontiers in measurement and assessment.pdf:pdf},
-publisher = {Oxford University Press},
-title = {{Biological diversity: frontiers in measurement and assessment}},
-year = {2011}
-}
-@article{Pavoine2007a,
-abstract = {The aim of this paper is to tackle the problem that arises from asymmetrical data cubes formed by two crossed factors fixed by the experimenter ( factor A and factor B, e. g., sites and dates) and a factor which is not controlled for ( the species). The entries of this cube are densities in species. We approach this kind of data by the comparison of patterns, that is to say by analyzing first the effect of factor B on the species-factor A pattern, and second the effect of factor A on the species-factor B pattern. The analysis of patterns instead of individual responses requires a correspondence analysis. We use a method we call Foucart's correspondence analysis to coordinate the correspondence analyses of several independent matrices of species x factor A ( respectively B) type, corresponding to each modality of factor B ( respectively A). Such coordination makes it possible to evaluate the effect of factor B ( respectively A) on the species-factor A ( respectively B) pattern. The results obtained by such a procedure are much more insightful than those resulting from a classical single correspondence analysis applied to the global matrix that is obtained by simply unrolling the data cube, juxtaposing for example the individual species 3 factor A matrices through modalities of factor B. This is because a single global correspondence analysis combines three effects of factors in a way that cannot be determined from factorial maps ( factor A, factor B, and factor A 3 factor B interaction) whereas the applications of Foucart's correspondence analysis clearly discriminate two different issues. Using two data sets, we illustrate that this technique proves to be particularly powerful in the analyses of ecological convergence which include several distinct data sets and in the analyses of spatiotemporal variations of species distributions.},
-author = {Pavoine, Sandrine and Blondel, Jacques and Baguette, Michel and Chessel, Daniel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2007 - A New Technique for Ordering Asymmetrical Three-Dimensional Data Sets in Ecology.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {512--523},
-title = {{A New Technique for Ordering Asymmetrical Three-Dimensional Data Sets in Ecology}},
-volume = {88},
-year = {2007}
-}
-@article{Barff1987,
-abstract = {The clustering of urban manufacturers occurs for a number of reasons; this paper focuses on the importance of production technology in understanding the degree of industrial clustering. The present analysis uses a sample of Cincinnati manufacturing plants to test several hypotheses that address the relationships between industrial clustering and industrial production technology. Most of the tests use second-order methods to distinguish between the spatial distributions of specified classes of industry. The analysis reveals that the functional disintegration of productive activity leads to increased degrees of industrial clustering in urban space. Furthermore, the dispersal that occurs through plant relocation is not a simple centrifugal process but a subtle modification of the clustered pattern of urban industry.},
-author = {Barff, R. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barff - 1987 - Industrial Clustering and the Organization of Production A Point Pattern Analysis of Manufacturing in Cincinnati, Ohio.pdf:pdf},
-journal = {Annals of the Association of American Geographers},
-number = {1},
-pages = {89--103},
-title = {{Industrial Clustering and the Organization of Production: A Point Pattern Analysis of Manufacturing in Cincinnati, Ohio}},
-url = {http://www.jstor.org/stable/2569204},
-volume = {77},
-year = {1987}
-}
-@article{Grabarnik2002,
-abstract = {A goodness-of-fit test statistic for spatial point processes is proposed and shown to have an asymptotic chi-squared distribution if the underlying point process is Poisson. Simulations demonstrate that the test, when testing for complete spatial randomness, is more sensitive to mixtures of regular and clustered point processes than the tests using the nearest neighbour distance distribution, the second- or third-order characteristics.},
-author = {Grabarnik, Pavel and Chiu, Sung Nok},
-doi = {10.1198/016214502388618735},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grabarnik, Chiu - 2002 - Goodness-of-fit test for complete spatial randomness against mixtures of regular and clustered spatial point pr.pdf:pdf},
-journal = {Biometrika},
-number = {2},
-pages = {411--421},
-title = {{Goodness-of-fit test for complete spatial randomness against mixtures of regular and clustered spatial point processes}},
-url = {http://dx.doi.org/10.1198/016214502388618735},
-volume = {89},
-year = {2002}
-}
-@article{Terborgh1985,
-abstract = {Describes the vegetation types of W Amazonia, where avian diversity is greatest, paying attention to the landscapes, vegetation structure, species diversity and succession within tropical moist forest and tropical wet forest regions. Organization of the bird community at Cocha Cashu, Manu National Park, SE Peru, is discussed, with reference to both species diversity and habitat selection, where structure, food resources and interspecific competition are key elements. -P.J.Jarvisavifauna Cocha Cashu Manu National Park Peru},
-author = {Terborgh, J},
-isbn = {0-12-178080-5},
-journal = {Habitat selection in birds},
-pages = {311--338},
-pmid = {1730},
-title = {{Habitat selection in Amazonian birds}},
-url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0022165376{\&}partnerID=40{\&}md5=cb58e5c4a23f0f93fdc5b472d245963e},
-year = {1985}
-}
-@article{Wiegand2017,
-abstract = {Spatial processes underlie major species coexistence mechanisms. A range of spatial analysis techniques are increasingly applied to data of fully mapped communities to quantify spatial structures in species and phylogenetic and functional diversity at some given spatial scale with the goal of gaining insights into processes of community assembly and dynamics. We review these techniques, including spatial point pattern analysis, quadrat-based analyses, and individual-based neighborhood models, and provide a practical roadmap for ecologists in the analysis of local spatial structures in species and phylogenetic and functional diversity. We show how scale-dependent metrics of spatial diversity can be used in concert with ecological null models, statistical models, and dynamic community simulation models to detect spatial patterns, reveal the influence of the biotic neighborhood on plant performance, and quantify the relative contribution of species interactions, habitat heterogeneity, and stochastic processe...},
-author = {Wiegand, Thorsten and Uriarte, Mar{\'{i}}a and Kraft, Nathan J. B. and Shen, Guochun and Wang, Xugao and He, Fangliang},
-doi = {10.1146/annurev-ecolsys-110316-022936},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand et al. - 2017 - Spatially Explicit Metrics of Species Diversity, Functional Diversity, and Phylogenetic Diversity Insights into.pdf:pdf},
-journal = {Annual Review of Ecology, Evolution, and Systematics},
-number = {1},
-pages = {329--351},
-title = {{Spatially Explicit Metrics of Species Diversity, Functional Diversity, and Phylogenetic Diversity: Insights into Plant Community Assembly Processes}},
-url = {http://www.annualreviews.org/doi/10.1146/annurev-ecolsys-110316-022936},
-volume = {48},
-year = {2017}
-}
-@article{Faddeev1956,
-author = {Faddeev, Dmitrii Konstantinovich},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faddeev - 1956 - On the concept of entropy of a finite probabilistic scheme.pdf:pdf},
-journal = {Uspekhi Mat. Nauk},
-number = {67},
-pages = {227--231},
-title = {{On the concept of entropy of a finite probabilistic scheme}},
-volume = {1},
-year = {1956}
-}
-@article{Vellend2001,
-abstract = {Indices of beta-diversity are of two major types, (1) those that measure among-plot variability in species composition independently of the position of individual plots on spatial or environmental gradients, and (2) those that measure the extent of change in species composition along predefined gradients, i.e. species turnover. Failure to recognize this distinction can lead to the inappropriate use of some beta-diversity indices to measure species turnover. Several commonly-used indices of beta-diversity are based on Whittaker's beta{\_}W ( beta{\_}W = gamma / alpha, where gamma is the number of species in an entire study area and alpha is the number of species per plot within the study area). It is demonstrated that these indices do not take into account the distribution of species on spatial or environmental gradients, and should therefore not be used to measure species turnover. The terms "beta-diversity" and "species turnover" should not be used interchangeably. Species turnover can be measured using matrices of compositional similarity and physical or environmental distances among pairs of study plots. The use of indices of beta-diversity and similarity-distance curves is demonstrated using simulated data sets.},
-author = {Vellend, Mark},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vellend - 2001 - Do commonly used indices of f-diversity measure species turnover.pdf:pdf},
-journal = {Journal of Vegetation Science},
-pages = {545--552},
-title = {{Do commonly used indices of f-diversity measure species turnover ?}},
-volume = {12},
-year = {2001}
-}
-@article{Callahan2016,
-abstract = {We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.},
-author = {Callahan, Benjamin J. and Mcmurdie, Paul J. and Rosen, Michael J. and Han, Andrew W. and Johnson, Amy Jo A. and Holmes, Susan P.},
-doi = {10.1038/nmeth.3869},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Callahan et al. - 2016 - DADA2 High resolution sample inference from amplicon data.pdf:pdf},
-journal = {Nature Methods},
-pages = {581--583},
-title = {{DADA2: High resolution sample inference from amplicon data}},
-url = {http://www.nature.com/nmeth/journal/v13/n7/full/nmeth.3869.html},
-volume = {13},
-year = {2016}
-}
-@article{Simberloff1976,
-abstract = {The equilibrium theory of island biogeography (1, 2) has found wide acceptance as a description of the organization of communities on oceanic and habitat islands (3).The basic premise is that the biota of any island is in dynamic equilibrium between immigration of species new to the island and local extinction of those already present. Extinction rates are believed to have a stochastic component, probabilities of local extinction presumably being inversely proportional to population size. Despite occasional data-based studies that appear not to demonstrate an immigration-extinction equilibrium (4-6), the equilibrium theory as just expressed has achieved the status of a paradigm. as used by Kuhn (7): a theory so widely accepted as an accurate description of nature that failure of an experiment to yield the result deduced from the theory leads not to rejection of the theory but rather to attempts to fault the deductive logic or experimental procedure, or simply to willful suspension of belief in the experimental result. As one example, equilibrium biogeography theory has been held to be important in vertebrate conservation planning (8) despite the fact that Lynch and Johnson (6) have severely impugned the primary avian basis for acceptance of the theory. Their result, however. is relegated to the status of "technical criticisms" by Sullivan and Shaffer (9) rather than used in a reexamination of the underlying theory. I shall attempt here to express the theory of equilibrium biogeography as a testable (falsifiable) hypothesis within the usual framework of hypothesis and deduction that has served the physical sciences (10)but has been often neglected in community ecology (11). I suggest also the kinds of evidence that could falsify the hypothesis, with some reference to the significance of partial or complete falsification. I also present new evidence from the mangrove island experiment (12-14) that was performed to test the theory of island biogeography.},
-author = {Simberloff, Daniel S.},
-doi = {10.1126/science.194.4265.572},
-journal = {Science},
-number = {4265},
-pages = {572--578},
-title = {{Species turnover and equilibrium island biogeography.}},
-volume = {194},
-year = {1976}
-}
-@article{Arroyo-Rodriguez2013,
-abstract = {Land-use change is the main driver of global biodiversity loss, but its relative impact on species turnover ($\beta$-diversity) across multiple spatial scales remains unclear. Plant communities in fragmented rain forests can undergo declines (floristic homogenization) or increases (floristic differentiation) in $\beta$-diversity. We tested these alternative hypotheses analysing a large vegetation data base from a hierarchically nested sampling design (450 plots in 45 forest patches in 3 landscapes with different deforestation levels) at Los Tuxtlas rain forest, Mexico. Differences in $\beta$-diversity across spatial scales (i.e. among plots, among patches, and among landscapes) were analysed using multiplicative diversity decompositions of Hill numbers. Plant $\beta$-diversity among plots within forest patches decreased in landscapes with higher deforestation levels, leading to floristic homogenization within patches. This homogenization process can be explained by the loss of rare and shade-tolerant plant species, and the recruitment and dominance of disturbance-adapted species, and can limit the accumulation of species ($\gamma$-diversity) in landscapes with higher deforestation. Nevertheless, the landscape with the highest deforestation level showed the highest floristic differentiation among patches. This landscape showed the greatest isolation distances between patches; a landscape spatial pattern that can limit the interchange of seeds (and species) between patches. Because the study patches are undergoing secondary succession following disturbances (e.g. logging, edge effects), different disturbance regimes and increased distance among patches could lead to higher $\beta$-diversity. Synthesis. These findings indicate that patterns of floristic homogenization and differentiation depend on the landscape configuration and on the spatial scale of analysis. At the landscape scale, our results suggest that, in accordance with non-equilibrium dynamics and the landscape-divergence hypothesis, patches located in landscapes with different forest cover and different connectivity can experience contrasting successional pathways due to increasing levels of compositional differentiation between patches. These novel findings add further uncertainties to the maintenance of biodiversity in severely deforested tropical landscapes and have key ecological implications for biodiversity conservation planning.},
-author = {Arroyo-Rodr{\'{i}}guez, V{\'{i}}ctor and R{\"{o}}s, Matthias and Escobar, Federico and Melo, Felipe P. L. and Santos, Br{\'{a}}ulio A. and Tabarelli, Marcelo and Chazdon, Robin L.},
-doi = {10.1111/1365-2745.12153},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arroyo-Rodr{\'{i}}guez et al. - 2013 - Plant $\beta$-diversity in fragmented rain forests testing floristic homogenization and differentiation hypot.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {1449--1458},
-title = {{Plant $\beta$-diversity in fragmented rain forests: testing floristic homogenization and differentiation hypotheses}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12153},
-volume = {101},
-year = {2013}
-}
-@article{Picard2004,
-abstract = {Various models of the relationship between area and number of resident species have been proposed. Most of them either ignore the spatial distribution of the species or suppose that they are spatially distributed at random. A new model is proposed that can deal with any type of spatial pattern, random, regular, or clustered, within the theory of point processes. It only requires that the distribution of the species be spatially homogeneous. The spatial pattern appears to modify the shape of the species-area curve as much as the species-abundance distribution. Mapped locations of trees and shrubs in a semi-arid savanna in Mali illustrate the theoretical developments, and an estimate of the expected number of species in the savanna is given. The observed number of species is consistent with the expected number, provided that the inventoried area remains spatially homogeneous.},
-author = {Picard, Nicolas and Karembe, M and Birnbaum, Philippe},
-doi = {10.1080/11956860.2004.11682808},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Picard, Karembe, Birnbaum - 2004 - Species-area curve and spatial pattern.pdf:pdf},
-journal = {Ecoscience},
-number = {1},
-pages = {45--54},
-title = {{Species-area curve and spatial pattern}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/11956860.2004.11682808},
-volume = {11},
-year = {2004}
-}
-@article{Barton2013,
-abstract = {Beta diversity is an important concept used to describe turnover in species composition across a wide range of spatial and temporal scales, and it underpins much of conservation theory and practice. Although substantial progress has been made in the mathematical and terminological treatment of different measures of beta diversity, there has been little conceptual synthesis of potential scale dependence of beta diversity with increasing spatial grain and geographic extent of sampling. Here, we evaluate different conceptual approaches to the spatial scaling of beta diversity, interpreted from ‘fixed' and ‘varying' perspectives of spatial grain and extent. We argue that a ‘sliding window' perspective, in which spatial grain and extent covary, is an informative way to conceptualize community differentiation across scales. This concept more realistically reflects the varying empirical approaches that researchers adopt in field sampling and the varying scales of landscape perception by different organisms. Scale dependence in beta diversity has broad implications for emerging fields in ecology and biogeography, such as the integration of fine-resolution ecogenomic data with large-scale macroecological studies, as well as for guiding appropriate management responses to threats to biodiversity operating at different spatial scales.},
-author = {Barton, Philip S. and Cunningham, Saul A. and Manning, Adrian D. and Gibb, Heloise and Lindenmayer, David B. and Didham, Raphael K.},
-doi = {10.1111/geb.12031},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barton et al. - 2013 - The spatial scaling of beta diversity.pdf:pdf},
-issn = {1466822X},
-journal = {Global Ecology and Biogeography},
-number = {6},
-pages = {639--647},
-title = {{The spatial scaling of beta diversity}},
-url = {http://doi.wiley.com/10.1111/geb.12031},
-volume = {22},
-year = {2013}
-}
-@article{Kuuluvainen1996,
-abstract = {The horizontal and vertical stand structure of living trees was examined in a managed and in a primeval spruce (Picea abies) dominated forest in southern Finland. Tree size distributions (diameter at breast height, DBH; tree height) were compared using frequency histograms. The vertical distribution of three heights was illustrated as tree height plots and quantified as the tree height diversity (THD) using the Shannon-Weaver formula. The horizontal spatial pattern of trees was described with stem maps and quantified with Ripley's K-function. The spatial autocorrelation of tree sizes was examined with semivariogram analysis. In the managed forest the DBH and height distributions of trees were bimodal, indicating a 2- layered vertical structure with a single dominant tree layer and abundant regeneration in the understorey. The primeval forest had a much higher total number of trees which were rather evenly distributed in different diameter and tree height classes. The K-function summaries for trees taller than 15 m indicated that the primeval stand had a close to completely random pattern. The managed stand was regular at small distances (up to 4 m). The semivariograms of tree sizes (DBH, tree height) showed that the managed forest had a clear spatial dependence in tree sizes up to inter-tree distances of about 12 m. In contrast, the primeval spruce forest had a variance peak at very short inter-tree distances ({\textless}1 m) and only weak spatial autocorrelation at short inter-tree distances (1-5 m). Excluding the understorey trees (height {\textless}15 m) from the analysis drastically changed the spatial structure of the forest as shown by semivariograms. In general, the structure of the primeval forest was both horizontally and vertically more variable and heterogeneous than the managed forest. The applicability of the methods used in describing fine-scale forest structure is discussed.},
-author = {Kuuluvainen, Timo and Penttinen, Antti and Leinonen, Kari and Nygren, Markku},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kuuluvainen et al. - 1996 - Statistical opportunities for comparing stand structural heterogeneity in managed and primeval forests an ex.pdf:pdf},
-journal = {Silva Fennica},
-number = {2-3},
-pages = {315--328},
-title = {{Statistical opportunities for comparing stand structural heterogeneity in managed and primeval forests: an example from boreal spruce forest in southern Finland}},
-url = {http://hdl.handle.net/1975/9243},
-volume = {30},
-year = {1996}
-}
-@article{Hsieh2014,
-abstract = {Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample-size- and coverage-based integrations of rarefaction (interpolation) and extrapolation (prediction) of Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages. We briefly review the conceptual background of Hill numbers along with two approaches to standardization. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity). Two types of biodiversity data are allowed: individual-based abundance data and sampling-unit-based incidence data. Several applications of the iNEXT packages are reviewed: (i) Non-asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage. Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.},
-author = {Hsieh, T. C. and Ma, K. H. and Chao, Anne},
-doi = {10.1111/2041-210X.12613},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hsieh, Ma, Chao - 2016 - iNEXT An R package for interpolation and extrapolation in measuring species diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-title = {{iNEXT: An R package for interpolation and extrapolation in measuring species diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12613/abstract},
-volume = {in press},
-year = {2016}
-}
-@techreport{Gini1913,
-author = {Gini, Corrado},
-title = {{Sulla misura della concentrazione e della variabilit{\`{a}} dei caratteri}},
-year = {1913}
-}
-@article{Ricotta2005,
-annote = {Cited By (since 1996):8
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: CEOCA
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, I-00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1556/ComEc.6.2005.2.12},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2005 - On parametric diversity indices in ecology A historical note.pdf:pdf},
-journal = {Community Ecology},
-number = {2},
-pages = {241--244},
-title = {{On parametric diversity indices in ecology: A historical note}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-30544453584{\&}partnerID=40{\&}md5=fda74c0d4367ec906971cddae267cfa8},
-volume = {6},
-year = {2005}
-}
-@incollection{Head2004,
-abstract = {This chapter examines empirical strategies that have been or could be used to evaluate the importance of agglomeration and trade models. This theoretical approach, widely known as “New Economic Geography” (NEG), emphasizes the interaction between transport costs and firm-level scale economies as a source of agglomeration. NEG focuses on forward and backward trade linkages as causes of observed spatial concentration of economic activity. We survey the existing literature, organizing the papers we discuss under the rubric of five interesting and testable hypotheses that emerge from NEG theory. We conclude the chapter with an overall assessment of the empirical support for NEG and suggest some directions for future research.},
-address = {Amsterdam},
-author = {Head, Keith and Mayer, Thierry},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Head, Mayer - 2004 - The Empirics of Agglomeration and Trade.pdf:pdf},
-pages = {56 p.},
-publisher = {Elsevier. North Holland},
-title = {{The Empirics of Agglomeration and Trade}},
-year = {2004}
-}
-@article{Rebertus1989a,
-abstract = {(1) The influence of fires on spatial pattern of Quercus laevis (turkey oak) growing on xeric sandhills in Florida was analysed using second-order L(t) functions. Monte Carlo tests were used to evaluate whether the observed patterns differed from complete spatial randomness and whether changes in pattern could be explained by random fire mortality. (2) Q. laevis trees in unburned sandhills were slightly clumped to randomly distributed at most scales. Initial fires tended to reduce the scale of maximum clumping, increase clumping intensity, create a more random to regular pattern at large scale, and increase segregation of Q. laevis and Pinus palustris (longleaf pine). Repeated fires at one-, two- and five-year intervals eventually left only a few clumps, which were protected from P. palustris along plot edges or near Q. geminata (sand live oak) groves. (3) In a reference plot unburned for twenty-one to twenty-five years, Q. laeois became more randomly distributed at all scales over a four-year period, and became slightly more aggregated with respect to P. palustris. (4) Patchiness of Q. laevis surviving fires was probably related to spatial variation in fire intensity, particularly with ‘hotspots' around P. palustris and protected areas near Q. geminata.},
-author = {Rebertus, A. J. and Williamson, G. Bruce and Moser, E. B.},
-doi = {10.2307/2260975},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rebertus, Williamson, Moser - 1989 - Fire-Induced Changes in Quercus Laevis Spatial Pattern in Florida Sandhills.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {638--650},
-title = {{Fire-Induced Changes in Quercus Laevis Spatial Pattern in Florida Sandhills}},
-url = {https://www.jstor.org/stable/2260975},
-volume = {77},
-year = {1989}
-}
-@article{Rysman2005,
-abstract = {This article proposes a statistical test for determining whether agents in discrete locations are more agglomerated or disperse than predicted by independent random choice.},
-author = {Rysman, Marc and Greenstein, Shane},
-doi = {10.1016/j.econlet.2004.07.021},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rysman, Greenstein - 2005 - Testing for agglomeration and dispersion.pdf:pdf},
-journal = {Economics Letters},
-pages = {405--411},
-title = {{Testing for agglomeration and dispersion}},
-url = {http://www.sciencedirect.com/science/article/pii/S0165176504003131},
-volume = {86},
-year = {2005}
-}
-@article{Roxburgh1998,
-abstract = {Many organisms display patchiness in their distribution patterns over a wide range of spatial scales. Patchy distribution patterns can be caused by processes such as growth, migration, reproduction, and mortality, which result in neighboring areas being more likely to contain a species than distant areas, a phenomenon known as positive spatial autocorrelation. When species are patchily distributed, the within-species spatial randomness assumptions of the standard statistical tests for detecting species associations are seriously violated. Using these tests under such circumstances can lead to incorrect rejection of the null hypothesis. To address this problem we introduce a new test for detecting species associations-the random patterns test. This test takes into account spatial autocorrelation by including the characteristics of the spatial pattern of each species into the null model. A randomization procedure was used to generate the null distribution of the test statistic. The random patterns test is illustrated with data collected from an herbaceous understory community of a Eucalyptus forest near Canberra, Australia.},
-author = {Roxburgh, Stephen H and Chesson, Peter},
-doi = {10.1890/0012-9658(1998)079[2180:ANMFDS]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roxburgh, Chesson - 1998 - A New Method for Detecting Species Associations with Spatially Autocorrelated Data.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {2180--2192},
-title = {{A New Method for Detecting Species Associations with Spatially Autocorrelated Data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(1998)079[2180:ANMFDS]2.0.CO;2/full},
-volume = {79},
-year = {1998}
-}
-@article{Weiher1999,
-abstract = {Ecologists need a common language of plant traits in order to make comparisons across regions and scales, pool data, and maximize the utility of the data. To develop such a set of traits we began with the primary challenges faced by plants: dispersal, establishment, and persistence in order to identify fundamental traits. Most of these traits are hard to measure, but advances in comparative ecology have suggested a number of easy to measure analogs. Unfortunately, some of the fundamental traits have no simple analog. The common core list includes: seed mass, seed shape, dispersal mode, clonality, specific leaf area, leaf water content, height, above- ground biomass, life history, onset of flowering, stem density, and resprouting ability. Most of the traits can be measured quantitatively, but several traits on the list must still be meas- ured qualitatively due to logistical problems or lack of an easy analog. Key problem areas include: dispersal ability, capacity for vegetative spread, germination, palatability, plasticity, and all the various below-ground traits. Comparative studies need to address these problem areas. The common core list is suggested as a common starting point for studies of functional ecology. The idiosyncrasies of regional floras and specific research agendas will dictate which traits can be ignored and those that need to be added. Keywords:},
-author = {Weiher, Evan and van der Werf, Adrie and Hompson, Ken and Roderick, Michael and Garnier, Eric and Eriksson, Ove},
-doi = {10.2307/3237076},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weiher et al. - 1999 - Challenging Theophrastus a common core list of plant traits for functional ecology.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {609--620},
-title = {{Challenging Theophrastus: a common core list of plant traits for functional ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3237076/full},
-volume = {10},
-year = {1999}
-}
-@article{Podani2007,
-abstract = {This paper is a response to Petchey and Gaston's criticism of our previous paper on the measurement of dendrogram-based functional diversity. In contrast to their suggestions, we insist that Euclidean distance is unsuitable to the analysis of variables with mixed scale types and maintain our earlier view that both the distance function and the clustering method can influence the dendrogram-based measure of functional diversity. We propose an extension of Gower's formula to accommodate nominal traits with non-exclusive categories and emphasize the necessity of the methodological standardization of functional diversity measures.},
-author = {Podani, J{\'{a}}nos and Schmera, D{\'{e}}nes},
-doi = {10.1111/j.2007.0030-1299.16160.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani, Schmera - 2007 - How should a dendrogram-based measure of functional diversity function A rejoinder to Petchey and Gaston.pdf:pdf},
-journal = {Oikos},
-number = {8},
-pages = {1427--1430},
-title = {{How should a dendrogram-based measure of functional diversity function? A rejoinder to Petchey and Gaston}},
-url = {http://doi.wiley.com/10.1111/j.2007.0030-1299.16160.x},
-volume = {116},
-year = {2007}
-}
-@incollection{Arbia2009,
-abstract = {The aim of this chapter is to present a class of statistical models to study the location of economic agents and their geographical concentration and explain their spatial interacting behaviour.},
-address = {Berlin},
-author = {Arbia, Giuseppe and Copetti, Massimiliano and Diggle, Peter J.},
-booktitle = {Growth and Innovation of Competitive Regions},
-doi = {10.1007/978-3-540-70924-4_14},
-editor = {Fratesi, Ugo and Senn, Lanfranco},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia, Copetti, Diggle - 2009 - Modelling Individual Behaviour of Firms in the Study of Spatial Concentration.pdf:pdf},
-isbn = {978-3-540-70924-4},
-pages = {297--327},
-publisher = {Springer},
-title = {{Modelling Individual Behaviour of Firms in the Study of Spatial Concentration}},
-url = {http://dx.doi.org/10.1007/978-3-540-70924-4{\_}14},
-year = {2009}
-}
-@article{Diggle1994,
-abstract = {We consider the problem of investigating the elevation in risk for a specified disease in relation to possible environmental factors. Our starting point is an inhomogeneous Poisson point process model for the spatial variation in the incidence of cases and controls in a designated geographic region, as proposed by Diggle. We develop a conditional approach to inference which converts the point process model to a non-linear binary regression model for the spatial variation in risk. Simulations suggest that the usual asymptotic approximations for likelihood-based inference are more reliable in this conditional setting than in the original point process setting. We present an application to some data on the spatial distribution of asthma in relation to three industrial locations.},
-author = {Diggle, Peter J. and Rowlingson, Barry S.},
-doi = {10.2307/2983529},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle, Rowlingson - 1994 - A Conditional Approach to Point Process Modeling of Elevated Risk.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {3},
-pages = {433--440},
-title = {{A Conditional Approach to Point Process Modeling of Elevated Risk}},
-url = {https://www.jstor.org/stable/2983529},
-volume = {157},
-year = {1994}
-}
-@article{Koen1991,
-abstract = {Confidence envelopes for Ripley's L function for N random points in the unit square were obtained by simulation. The 90, 95 and 99th percentiles of 1000 simulations are given in tabular form for N in the range 10 to 350. Results for a number of choices of the maximum interpoint distance are reported.},
-author = {Koen, C.},
-doi = {10.1002/bimj.4710330206},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Koen - 1991 - Approximate confidence bounds for Ripley's statistic for random points in a square.pdf:pdf},
-journal = {Biometrical Journal},
-number = {2},
-pages = {173--177},
-title = {{Approximate confidence bounds for Ripley's statistic for random points in a square}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/bimj.4710330206/abstract},
-volume = {33},
-year = {1991}
-}
-@article{Fung2015,
-abstract = {Ecological communities are subjected to stochasticity in the form of demo- graphic and environmental variance. Stochastic models that contain only demographic variance (neutral models) provide close quantitative fits to observed species- abundance distributions (SADs) but substantially underestimate observed temporal species- abundance fluctuations. To provide a holistic assessment of whether models with demographic and environmental variance perform better than neutral models, the fit of both to SADs and temporal species- abundance fluctuations at the same time has to be tested quantitatively. In this study, we quantitatively test how closely a model with demographic and environ- mental variance reproduces total numbers of species, total abundances, SADs and temporal species- abundance fluctuations for two tropical forest tree communities, using decadal data from long- term monitoring plots and considering individuals larger than two size thresholds for each community. We find that the model can indeed closely reproduce these static and dynamic patterns of biodiversity in the two communities for the two size thresholds, with better overall fits than corresponding neutral models. Therefore, our results provide evidence that stochastic models incorporating demographic and environmental variance can simultaneously capture important static and dynamic biodiversity patterns arising in tropical forest communities.},
-author = {Fung, Tak and O'Dwyer, James P. and Rahman, Kassam Abd. and Fletcher, Christine D. and Chisholm, Ryan A.},
-doi = {10.1890/15-0984.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fung et al. - 2015 - Reproducing static and dynamic biodiversity patterns in tropical forests the critical role of environmental varianc.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1207--1217},
-title = {{Reproducing static and dynamic biodiversity patterns in tropical forests: the critical role of environmental variance}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/15-0984.1/abstract},
-volume = {97},
-year = {2015}
-}
-@article{Kulldorff2006,
-abstract = {In many applications, it is of interest to test whether a spatial point pattern is randomly generated after adjusting for an underlying spatial inhomogeneity. A great variety of different test statistics have been proposed for this purpose by scientists in different fields; these are reviewed in this article. Despite apparent dissimilarities in terms of their original formulations, most of these statistics can be placed into one general framework of which they are special cases. This makes it easier to see exactly how they relate to one another and also to determine which test to use for a particular application. The general framework can also be used for proposing new tests by combining properties of existing tests, for developing theoretical foundations for these types of test statistics, for doing structured comparative evaluations, and for software development.},
-author = {Kulldorff, Martin},
-doi = {10.1198/016214506000000618},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kulldorff - 2006 - Tests of Spatial Randomness Adjusted for an Inhomogeneity.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {475},
-pages = {1289--1305},
-title = {{Tests of Spatial Randomness Adjusted for an Inhomogeneity}},
-url = {http://pubs.amstat.org/doi/abs/10.1198/016214506000000618{\%}5Cnhttp://www.tandfonline.com/doi/abs/10.1198/016214506000000618},
-volume = {101},
-year = {2006}
-}
-@article{Manter2015,
-abstract = {Motivation: In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo $\beta$-diversity. Results: We present a set of tools to identify and correct for the presence of pseudo $\beta$-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo $\beta$-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo $\beta$-diversity in pairwise community contrasts.},
-author = {Manter, Daniel K. and Bakker, Matthew G.},
-doi = {10.1093/bioinformatics/btv394},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Manter, Bakker - 2015 - Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and.pdf:pdf},
-journal = {Bioinformatics},
-number = {21},
-pages = {3451--3459},
-title = {{Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff}},
-url = {http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/bioinformatics/btv394},
-volume = {31},
-year = {2015}
-}
-@article{Esty1983,
-abstract = {The coverage of a multinomial random sample is the sum of the probabilities of the observed classes. A normal limit law is rigorously proved for Good's (1953) coverage estimator. The result is valid under very general conditions and all terms except the coverage itself are observable. Nevertheless the implied confidence intervals are not much wider than those developed under restrictive assumptions such as in the classical occupancy problem. The asymptotic variance is somewhat unexpected. The proof utilizes a method of Holst (1979).},
-author = {Esty, Warren W},
-doi = {10.2307/2240652},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Esty - 1983 - A Normal Limit Law for a Nonparametric Estimator of the Coverage of a Random Sample.pdf:pdf},
-journal = {The Annals of Statistics},
-number = {3},
-pages = {905--912},
-title = {{A Normal Limit Law for a Nonparametric Estimator of the Coverage of a Random Sample}},
-url = {http://www.jstor.org/stable/2240652},
-volume = {11},
-year = {1983}
-}
-@article{Louf2013,
-abstract = {One of the most important features of spatial networks-such as transportation networks, power grids, the Internet, and neural networks-is the existence of a cost associated with the length of links. Such a cost has a profound influence on the global structure of these networks, which usually display a hierarchical spatial organization. The link between local constraints and large-scale structure is not elucidated, however, and we introduce here a generic model for the growth of spatial networks based on the general concept of cost-benefit analysis. This model depends essentially on a single scale and produces a family of networks that range from the star graph to the minimum spanning tree and are characterized by a continuously varying exponent. We show that spatial hierarchy emerges naturally, with structures composed of various hubs controlling geographically separated service areas, and appears as a large-scale consequence of local cost-benefit considerations. Our model thus provides the basic building blocks for a better understanding of the evolution of spatial networks and their properties. We also find that, surprisingly, the average detour is minimal in the intermediate regime as a result of a large diversity in link lengths. Finally, we estimate the important parameters for various world railway networks and find that, remarkably, they all fall in this intermediate regime, suggesting that spatial hierarchy is a crucial feature for these systems and probably possesses an important evolutionary advantage.},
-archivePrefix = {arXiv},
-arxivId = {1305.3282},
-author = {Louf, R{\'{e}}mi and Jensen, Pablo and Barthelemy, Marc},
-doi = {10.1073/pnas.1222441110},
-eprint = {1305.3282},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Louf, Jensen, Barthelemy - 2013 - Emergence of hierarchy in cost-driven growth of spatial networks.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {22},
-pages = {8824--8829},
-title = {{Emergence of hierarchy in cost-driven growth of spatial networks}},
-url = {http://www.pnas.org/content/110/22/8824.full},
-volume = {110},
-year = {2013}
-}
-@article{Swenson2013,
-abstract = {Tropical tree communities present one of the most challenging systems for studying the processes underlying community assembly. Most community assembly hypotheses consider the relative importance of the ecological similarity of co-occurring species. Quantifying this similarity is a daunting and potentially impossible task in species-rich assemblages. During the past decade tropical tree ecologists have increasingly utilized phylogenetic trees and functional traits to estimate the ecological similarity of species in order to test mechanistic community assembly hypotheses. A large amount of work has resulted with many important advances having been made along the way. That said, there are still many outstanding challenges facing those utilizing phylogenetic and functional trait approaches to study community assembly. Here I review the conceptual background, major advances and major remaining challenges in phylogenetic- and trait-based approaches to community ecology with a specific focus on tropical trees. I argue that both approaches tremendously improve our understanding of tropical tree community ecology, but neither approach has fully reached its potential thus far.},
-author = {Swenson, Nathan G.},
-doi = {10.1111/j.1600-0587.2012.00121.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/De Bello et al. - 2013 - Which trait dissimilarity for functional diversity Trait means or trait overlap.pdf:pdf},
-journal = {Ecography},
-number = {3},
-title = {{The assembly of tropical tree communities - the advances and shortcomings of phylogenetic and functional trait analyses}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2012.00121.x/abstract},
-volume = {36},
-year = {2013}
-}
-@article{Hanisch1983,
-abstract = {For a hard-core clustering point-process different methods of estimating the model parameters are discussed. Using a relation to spatial birth-and-death processes a solution of a prediction problem is suggested. Three examples are considered.},
-author = {Hanisch, B. J. and Stoyan, Dietrich},
-doi = {10.1080/03610928308801736},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hanisch, Stoyan - 1983 - Remarks on statistical inference and prediction for a hard-core clustering model.pdf:pdf},
-journal = {Statistics},
-pages = {559--567},
-title = {{Remarks on statistical inference and prediction for a hard-core clustering model}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/03610928308801736},
-volume = {14},
-year = {1983}
-}
-@article{Ilic2013,
-abstract = {In this comment, we consider a generalization of the Shannon–Khinchin axioms (GSK axioms) and the uniqueness theorem for the entropy determined by GSK axioms proposed in [H. Suyari, IEEE Trans. Inf. Theory, vol. 50, pp. 1783–1787, Aug. 2004]. It is shown that the class of entropy functions determined by the axioms from the mentioned paper is wider than the one proposed in this paper, and a counterexample is given. We also derive a new class of entropies by fixing the incorrectness which occurs in the mentioned paper.},
-author = {Ili{\'{c}}, Velimir M. and Stankovi{\'{c}}, Miomir and Mulali{\'{c}}, Edin H.},
-doi = {10.1109/TIT.2013.2259958},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ili{\'{c}}, Stankovi{\'{c}}, Mulali{\'{c}} - 2013 - Comments on Generalization of Shannon-Khinchin Axioms to Nonextensive Systems and the Uniqueness Theor.pdf:pdf},
-journal = {IEEE Transactions on Information Theory},
-number = {10},
-pages = {6950--6952},
-title = {{Comments on "Generalization of Shannon-Khinchin Axioms to Nonextensive Systems and the Uniqueness Theorem for the Nonextensive Entropy"}},
-url = {http://ieeexplore.ieee.org/document/6517927/},
-volume = {59},
-year = {2013}
-}
-@article{Diggle1991,
-abstract = {Motivated by recent interest in the possible spatial clustering of rare diseases, the paper develops an approach to the assessment of spatial clustering based on the second-moment properties of a labelled point process. The concept of no spatial clustering is identified with the hypothesis that in a realisation of a stationary spatial point process consisting of events of two qualitatively different types, the type 1 events are a random sample from the superposition of type 1 and type 2 events. A diagnostic plot for estimating the nature and physical scale of clustering effects is proposed. The availability of Monte Carlo tests of significance is noted. An application to published data on the spatial distribution of childhood leukaemia and lymphoma in North Humberside is described},
-author = {Diggle, Peter J. and Chetwynd, A. G.},
-doi = {10.2307/2532668},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle, Chetwynd - 1991 - Second-Order Analysis of Spatial Clustering for Inhomogeneous Populations.pdf:pdf},
-journal = {Biometrics},
-number = {3},
-pages = {1155--1163},
-title = {{Second-Order Analysis of Spatial Clustering for Inhomogeneous Populations}},
-url = {http://www.jstor.org/stable/2532668},
-volume = {47},
-year = {1991}
-}
-@article{Kortchagina2005,
-abstract = {La Russie a connu une histoire contemporaine unique, fertile en {\'{e}}volutions politiques et {\'{e}}conomiques. Plusieurs crises conjoncturelles r{\'{e}}centes importantes (1992, 1998) ont eu pour cons{\'{e}}quence une chute de grande ampleur des niveaux de vie (division par deux en 1992). Le bilan d{\'{e}}mographique r{\'{e}}sume bien l'{\'{e}}tat actuel de la situation, celle d'une ind{\'{e}}niable crise, mais avec des signes r{\'{e}}cents d'am{\'{e}}lioration. L'esp{\'{e}}rance de vie pour les hommes n'est plus que de 58,8 ans, en baisse de 5 ans par rapport {\`{a}} 1990 ; pour les femmes, elle est d{\'{e}}sormais de 72 ans, soit 2 ans de moins qu'il y a une douzaine d'ann{\'{e}}es. La mortalit{\'{e}} infantile reste {\`{a}} un niveau {\'{e}}lev{\'{e}} par rapport aux pays de l'Europe de l'Ouest, mais elle est en constante diminution. Globalement la population a tendance {\`{a}} diminuer. Divortialit{\'{e}} {\'{e}}lev{\'{e}}e et cohabitation entre g{\'{e}}n{\'{e}}rations pour r{\'{e}}soudre les probl{\`{e}}mes de raret{\'{e}} des logements expliquent la fr{\'{e}}quence {\'{e}}lev{\'{e}}e des familles monoparentales et des m{\'{e}}nages complexes. Le passage vers l'{\'{e}}conomie de march{\'{e}} a boulevers{\'{e}} le march{\'{e}} du travail. Mais le ch{\^{o}}mage, apr{\`{e}}s avoir cr{\^{u}}, a diminu{\'{e}} dans les ann{\'{e}}es r{\'{e}}centes ; le taux actuel (7,9 {\%}) est plut{\^{o}}t inf{\'{e}}rieur {\`{a}} ce que l'on observe dans les autres pays en transition, r{\'{e}}sultat d'une politique qui a pr{\'{e}}f{\'{e}}r{\'{e}} substituer {\`{a}} du ch{\^{o}}mage potentiel une baisse des salaires r{\'{e}}els. Cons{\'{e}}quence de l'inflation galopante qui a marqu{\'{e}} la d{\'{e}}cennie 1991-2001, le salaire r{\'{e}}el moyen de 2004 est {\`{a}} peine sup{\'{e}}rieur {\`{a}} la moiti{\'{e}} de ce qu'il {\'{e}}tait en 1991. L'{\'{e}}cart est moindre au niveau de l'ensemble des revenus, qui ont davantage profit{\'{e}} de la reprise r{\'{e}}cente : en 2004, les revenus moyens repr{\'{e}}sentent 83 {\%} de ce qu'ils {\'{e}}taient en 1991. Plus de la moiti{\'{e}} du budget est d{\'{e}}sormais consacr{\'{e}}e {\`{a}} l'alimentation. M{\^{e}}me si l'importance relative des prestations sociales a cr{\^{u}} l{\'{e}}g{\`{e}}rement, dans les conditions actuelles de restrictions budg{\'{e}}taires, l'acc{\`{e}}s aux soins et {\`{a}} l'instruction n'est pas garanti pour tous. Cette baisse des revenus s'est accompagn{\'{e}}e d'une augmentation de l'in{\'{e}}galit{\'{e}} et de la pauvret{\'{e}} : les familles monoparentales, les familles nombreuses et les personnes {\^{a}}g{\'{e}}es font face {\`{a}} des conditions de vie particuli{\`{e}}rement d{\'{e}}favorables, surtout dans les petites villes, signe d'une polarisation croissante entre Moscou d'une part et les villes de province, surtout les plus petites d'entre elles d'autre part.},
-author = {Kortchagina, Irina and Ovtcharova, Lilia and Prokofieva, Lidia and Festy, Patrick and Verger, Daniel},
-doi = {10.3406/estat.2005.7201},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kortchagina et al. - 2005 - Conditions de vie et pauvret{\'{e}} en Russie.pdf:pdf},
-journal = {Economie et Statistique},
-number = {1},
-pages = {219--244},
-title = {{Conditions de vie et pauvret{\'{e}} en Russie}},
-url = {http://www.persee.fr/web/revues/home/prescript/article/estat{\_}0336-1454{\_}2005{\_}num{\_}383{\_}1{\_}7201},
-volume = {383},
-year = {2005}
-}
-@article{Wang2010,
-abstract = {We propose a Poisson-compound gamma approach for species richness estimation. Based on the denseness and nesting properties of the gamma mixture, we fix the shape parameter of each gamma component at a unified value, and estimate the mixture using nonparametric maximum likelihood. A least-squares crossvalidation procedure is proposed for the choice of the common shape parameter. The performance of the resulting estimator of N is assessed using numerical studies and genomic data.},
-author = {Wang, Ji-Ping},
-doi = {10.1093/biomet/asq026},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wang - 2010 - Estimating species richness by a Poisson-compound gamma model.pdf:pdf},
-journal = {Biometrika},
-number = {3},
-pages = {727--740},
-title = {{Estimating species richness by a Poisson-compound gamma model}},
-url = {http://biomet.oxfordjournals.org/content/97/3/727.abstract},
-volume = {97},
-year = {2010}
-}
-@article{Kosman2013,
-abstract = {Making inferences about variation within and among various operational units may depend on the ability of a selected approach to diversity analysis to utilize correctly all information available in the rawdata. Frequency-based genotypic and gene diversity parameters, methods of ‘true diversity' and functional diversity, as well as two types of dissimilarity based approaches (by means of averaging pairwise dissimilarities, and solution of the assignment problem) are comprehensively discussed. The dissimilarity based approaches need a suitable assessment of dissimilarity between individual operational units (individuals, communities, populations, clusters, functions, phylogenetic trees etc.). Many commonly used diversity parameters can be derived in terms of the average based measures. The assignment based methods are able to address some limitations and shortcomings of the commonly used measures of population diversity, and they are preferable in the case of possible association between traits. They are always mathematically valid,whereas validity of the average based methods depends on the selected dissimilarity measure. The dissimilarity based methods actually assess functional diversity in the space of the selected traits, and they allow measuring complex diversity and assessment of total gamma-diversity as the sum of the independent components of a-and {\ss}-diversity with descriptors of different types. The dissimilarity based method for diversity analysis can be consistently employed together with other approaches to data analysis (e.g. clustering). In particular, they may provide valid diversity estimates and replace Nei's diversity measures, which are often inconsistently used with binary molecular marker data.},
-author = {Kosman, Evsey},
-doi = {10.1007/s10658-013-0323-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosman - 2013 - Measuring diversity from individuals to populations.pdf:pdf},
-journal = {European Journal of Plant Pathology},
-number = {3},
-pages = {467--486},
-title = {{Measuring diversity: from individuals to populations}},
-url = {http://link.springer.com/10.1007/s10658-013-0323-3},
-volume = {138},
-year = {2013}
-}
-@article{Gotzenberger2016,
-abstract = {Questions Mechanisms of community assembly are increasingly explored by combining community and species trait data with null models. By investigating if the traits of co-existing species are more similar (trait convergence) or more dissimilar (trait divergence) than expected by chance, these tests relate observed patterns to different co-existence mechanisms. Do null models accurately detect trait convergence and divergence? Are different null models equally good at detecting these two opposing patterns? How important are the species pool and other constraints that are considered by different null models? Methods We applied ten common randomizations to communities that were simulated in a process-based model. Results Null models good at detecting biotic processes differed from those null models that revealed abiotic processes. In particular, limiting similarity (detected through divergence) was better detected by randomizations that release the link between species abundance and trait values, whereas environmental filtering (detected through convergence of an environmental response trait) was identified by randomizations that keep this link. In general, using species abundance data provided better results than using presence–absence data, particularly within given limited environmental conditions. Weaker competitor exclusion (detected through convergence of a competition-related trait) was only detected when no environmental filtering was acting on the simulated assembly, which points to difficulties in disentangling biotic and abiotic convergence in natural communities, especially when data are randomized across habitats. Conclusions Overall the results manifest the importance of the pool of species over which randomizations are applied; in particular whether randomizations are conducted across or within given habitats. Taken together, our findings show that different null models must be combined and applied to a carefully chosen pool of species and species abundance data to ensure that co-existence mechanisms can be properly assessed. We utilize the results to (1) discuss how different constraints implied in the different null models affect the outcomes of our tests, and (2) provide some basic recommendations on how to choose null models, given the data available and questions being asked.},
-author = {G{\"{o}}tzenberger, Lars and Botta-Duk{\'{a}}t, Zolt{\'{a}}n and Lep{\v{s}}, Jan and P{\"{a}}rtel, Meelis and Zobel, Martin and de Bello, Francesco},
-doi = {10.1111/jvs.12452},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/G{\"{o}}tzenberger et al. - 2016 - Which randomizations detect convergence and divergence in trait-based community assembly A test of commonly.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {1275--1287},
-title = {{Which randomizations detect convergence and divergence in trait-based community assembly? A test of commonly used null models}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/jvs.12452/abstract},
-volume = {27},
-year = {2016}
-}
-@article{Head1995,
-abstract = {Recent theories of economic geography suggest that firms in the same industry may be drawn to the same locations because proximity generates positive externalities or ‘agglomeration effects'. Under this view, chance events and government inducements can have a lasting influence on the geographical pattern of manufacturing. However, most evidence on the causes and magnitude of industry localization has been based on stories, rather than statistics. This paper examines the location choices of 751 Japanese manufacturing plants built in the United States since 1980. Conditional logit estimates support the hypothesis that industry-level agglomeration benefits play an important role in location decisions.},
-author = {Head, Keith and Ries, John and Swenson, Deborah},
-doi = {10.1016/0022-1996(94)01351-R},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Head, Ries, Swenson - 1995 - Agglomeration Benefits and Location Choice Evidence from Japanese Manufacturing Investments in the United S.pdf:pdf},
-journal = {Journal of International Economics},
-number = {3-4},
-pages = {223--247},
-title = {{Agglomeration Benefits and Location Choice: Evidence from Japanese Manufacturing Investments in the United States}},
-url = {http://www.sciencedirect.com/science/article/pii/002219969401351R},
-volume = {38},
-year = {1995}
-}
-@article{Volkov2006,
-author = {Volkov, Igor and Banavar, Jayanth R. and He, Fangliang and Hubbell, Stephen P. and Maritan, Amos},
-doi = {10.1038/nature04827},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Volkov et al. - 2006 - Theoretical biology - Comparing models of species abundance - Reply.pdf:pdf},
-journal = {Nature},
-number = {7089},
-pages = {E1--E2},
-title = {{Theoretical biology - Comparing models of species abundance - Reply}},
-url = {http://www.nature.com/nature/journal/v441/n7089/abs/nature04827.html},
-volume = {441},
-year = {2006}
-}
-@techreport{Wickelmaier2003,
-abstract = {Multidimensional scaling (MDS) is a classical approach to the problem of nding underlying attributes or dimensions, which in uence how subjects evaluate a given set of objects or stimuli. This paper provides a brief introduction to MDS. Its basic applications are outlined by several examples. For the interested reader a short overview of recommended literature is appended. The purpose of this paper is to facilitate the rst contact with MDS to the non-statistician.},
-author = {Wickelmaier, Florian},
-doi = {10.1080/13546800903126016},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wickelmaier - 2003 - An introduction to MDS.pdf:pdf},
-title = {{An introduction to MDS}},
-url = {http://steep.inrialpes.fr/{\%}7B{~}{\%}7DArnaud/indexation/mds03.pdf},
-year = {2003}
-}
-@incollection{Waller2010,
-author = {Waller, Lance},
-booktitle = {Handbook in Spatial Statistics},
-chapter = {Chapter 22},
-editor = {{A.E.Gelfand P. Guttorp, M. Fuentes}, P Diggle},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Waller - 2010 - Point Process Models and Methods in Spatial Epidemiology.pdf:pdf},
-publisher = {Chapman {\&} Hall},
-title = {{Point Process Models and Methods in Spatial Epidemiology}},
-year = {2010}
-}
-@article{Lamberti2003,
-abstract = {The Jensen–Shannon divergence is a symmetrized and smoothed version of the Kullback–Leibler divergence. Recently it has been widely applied to the analysis and characterization of symbolic sequences. In this paper we investigate a generalization of the Jensen–Shannon divergence. This generalization is done in the framework of the non-extensive Tsallis statistics. We study its basic properties and we investigate its applicability as a tool for segmentating symbolic sequences.},
-author = {Lamberti, Pedro W. and Majtey, Ana P.},
-doi = {http://dx.doi.org/10.1016/S0378-4371(03)00566-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lamberti, Majtey - 2003 - Non-logarithmic Jensen–Shannon divergence.pdf:pdf},
-journal = {Physica A},
-number = {1–2},
-pages = {81--90},
-title = {{Non-logarithmic Jensen–Shannon divergence}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378437103005661},
-volume = {329},
-year = {2003}
-}
-@article{Grau2002,
-abstract = {Recent community studies found no relationship between treefall regime and species richness at the scale of individual treefalls. Here, spatial patterns of trees {\textgreater}5 cm diameter and treefalls (mostly dated by using dendroecological techniques) were described in 6 ha of subtropical montane forest in northwest Argentina, to explore the relationships between treefalls and tree community composition at different spatial scales. Time since gap formation showed spatial autocorrelation at spatial scales smaller than 5000 m(2) (Moran's I coefficient). Point pattern analysis (Ripley's K function),showed that very recent treefalls (1990-1997) are spatially associated with previous treefalls (1978-1987) at scales of 10005000 m(2). At the scale of individual treefalls (100-400 m(2)), species richness was uncorrelated with treefall regime, and shade-tolerant and light-demanding species were not discriminated in a multidimensional scaling ordination analysis. However, correlation between treefalls and species richness, and the discrimination of regeneration groups, increased abruptly at the scales of treefall aggregations. In agreement with previous studies, this study suggests that isolated treefalls have little effect on species composition and diversity, probably due to recruitment limitation. Instead, this study shows that at scales {\textgreater} 1000 m(2), treefall regime is a good predictor of species richness and composition of regeneration groups. This may be because treefall aggregations and gap expansion increase the probability of new nearby treefalls being colonized by light-demanding species. These results emphasize the importance of scale and spatial dynamics of disturbances and species dispersal in the study of canopy disturbances and their effects on community composition and diversity.},
-annote = {Article
-English
-ECOLOGY
-596FQ},
-author = {Grau, H{\'{e}}ctor Ricardo},
-doi = {10.1890/0012-9658(2002)083[2591:SDRBTA]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grau - 2002 - Scale-dependent relationships between treefalls and species richness in a neotropical montane forest.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2591--2601},
-title = {{Scale-dependent relationships between treefalls and species richness in a neotropical montane forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2002)083[2591:SDRBTA]2.0.CO;2/abstract},
-volume = {83},
-year = {2002}
-}
-@article{Bacaro2012,
-abstract = {The central role of beta diversity in describing biodiversity patterns has been investigated in many fields of ecology and biogeography. While a variety of measures of beta diversity have been proposed over the past five decades, the question of how to test for differences in beta diversity among different sets of sampling plots has been addressed only rarely. Here, we describe a simple analytical procedure to test for differences in beta diversity among distinct sets of plots. The advantage of this approach compared to methods that have been previously proposed lies in its randomization procedure. Such a procedure creates a distribution of null values of the test statistic that is compatible with the null hypothesis of no significant difference in multivariate dispersion between the groups. The proposed test was illustrated using a large dataset of plant and water beetle (Coleoptera) assemblages collected from 45 farmland ponds in Ireland.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: ECRSE
-Language of Original Document: English
-Correspondence Address: Bacaro, G.; BIOCONNET, Biodiversity and Conservation Network, Department of Environmental Science G. Sarfatti, University of Siena, Via P. A. Mattioli 4, 53100 Siena, Italy; email: bacaro@unisi.it},
-author = {Bacaro, Giovanni and Gioria, Margherita and Ricotta, Carlo},
-doi = {10.1007/s11284-011-0899-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro, Gioria, Ricotta - 2012 - Testing for Differences in Beta Diversity From Plot-To-Plot Dissimilarities.pdf:pdf},
-journal = {Ecological Research},
-number = {2},
-pages = {285--292},
-title = {{Testing for Differences in Beta Diversity From Plot-To-Plot Dissimilarities}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84858792371{\&}partnerID=40{\&}md5=7fe17fe8798e227dd7e4c2bb446c753b},
-volume = {27},
-year = {2012}
-}
-@article{GAUSE1936,
-abstract = {(With Four Text-figures.) ALTHOUGH the phenomena of variation and heredity have in recent years become amenable to quantitative treatment, our knowledge of the struggle for existence has been increased to an almost negligible extent during the past fifty years. In the ...},
-author = {Gause, G. F.},
-doi = {10.1097/00010694-193602000-00018},
-isbn = {0486495205},
-issn = {0038-075X},
-journal = {Soil Science},
-number = {2},
-pages = {159},
-pmid = {1038},
-title = {{The Struggle for Existence}},
-url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage{\&}an=00010694-193602000-00018},
-volume = {41},
-year = {1936}
-}
-@article{Benassy1996,
-abstract = {Devereux et al. (Economics Letters, 1993, 41, 57-61) showed that introducing together imperfect competition and increasing returns to specialization into Real Business Cycle (RBC)-type models results in making output more persistent than the underlying technology shocks. We carry out a simple generalization of their model, which clearly disentangles the two features, and show that the added persistence is actually because of the increasing returns to specialization.},
-author = {B{\'{e}}nassy, Jean-Pascal},
-doi = {10.1016/S0165-1765(96)00856-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/B{\'{e}}nassy - 1996 - Monopolistic competition, increasing returns to specialization and output persistence.pdf:pdf},
-journal = {Economics Letters},
-number = {2},
-pages = {187--191},
-title = {{Monopolistic competition, increasing returns to specialization and output persistence}},
-url = {http://www.sciencedirect.com/science/article/pii/S0165176596008567},
-volume = {52},
-year = {1996}
-}
-@article{Hoorn2010a,
-abstract = {The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.},
-author = {Hoorn, C and Wesselingh, F.P. and ter Steege, H. and Bermudez, M.A. and Mora, A. and Sevink, J. and Sanmart{\'{i}}n, I. and Sanchez-Meseguer, A. and Anderson, C.L. and Figueiredo, J.P. and Jaramillo, C. and Riff, D. and Negri, F.R. and Hooghiemstra, H. and Lundberg, J. and Stadler, T. and S{\"{a}}rkinen, T. and Antonelli, A.},
-doi = {10.1126/science.1194585},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hoorn et al. - 2010 - Amazonia Through Time Andean.pdf:pdf},
-isbn = {1095-9203 (Electronic) 0036-8075 (Linking)},
-issn = {1095-9203},
-journal = {Science},
-number = {November},
-pages = {927--931},
-pmid = {21071659},
-title = {{Amazonia Through Time : Andean}},
-volume = {330},
-year = {2010}
-}
-@article{Letten2014,
-abstract = {An increasingly popular practice in community ecology is to use the evolutionary distance among interacting species as a proxy for their overall functional similarity. At the core of this approach is the implicit, yet poorly recognized, assumption that trait dissimilarity increases linearly with divergence time, that is all evolutionary time is considered equal. However, given a classic Brownian model of trait evolution, we show that the expected functional displacement of any two taxa is more appropriately represented as a linear function of time's square root. In light of this mismatch between theory and methodology, we argue that current methods at the interface of ecology and evolutionary biology often greatly overweight deep time relative to recent time. An easy solution to this weighting problem is a square root transformation of the phylogenetic distance matrix. Using simulated models of trait evolution and community assembly, we show that this transformation yields considerably higher statistical power, with improvements in 92{\%} of trials. This methodological update is likely to improve our understanding of the connection between evolutionary relatedness and contemporary ecological processes.},
-author = {Letten, Andrew D. and Cornwell, William K.},
-doi = {10.1111/2041-210X.12237},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Letten, Cornwell - 2014 - Trees, branches and (square) roots why evolutionary relatedness is not linearly related to functional distance.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {4},
-pages = {439--444},
-title = {{Trees, branches and (square) roots: why evolutionary relatedness is not linearly related to functional distance}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12237},
-volume = {6},
-year = {2015}
-}
-@article{Chao1987,
-abstract = {A point estimator and its associated confidence interval for the size of a closed population are proposed under models that incorporate heterogeneity of capture probability. Real data sets provided in Edwards and Eberhardt (1967, Journal of Wildlife Management 31, 87-96) and Carothers (1973, Journal of Animal Ecology 42, 125-146) are used to illustrate this method and to compare it with other estimates. The performance of the proposed procedure is also investigated by means of Monte Carlo experiments. The method is especially useful when most of the captured individuals were caught once or twice in the sample, for which case the jackknife estimator usually does not work well. Numerical results also show that the proposed confidence interval performs satisfactorily in maintaining the nominal levels.},
-author = {Chao, Anne},
-doi = {10.2307/2531532},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao - 1987 - Estimating the population size for capture-recapture data with unequal catchability.pdf:pdf},
-journal = {Biometrics},
-number = {4},
-pages = {783--791},
-title = {{Estimating the population size for capture-recapture data with unequal catchability}},
-url = {https://www.jstor.org/stable/2531532},
-volume = {43},
-year = {1987}
-}
-@article{Cardinale2012,
-abstract = {The most unique feature of Earth is the existence of life, and the most extraordinary feature of life is its diversity. Approximately 9 million types of plants, animals, protists and fungi inhabit the Earth. So, too, do 7 billion people. Two decades ago, at the first Earth Summit, the vast majority of the world's nations declared that human actions were dismantling the Earth's ecosystems, eliminating genes, species and biological traits at an alarming rate. This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper.},
-annote = {Cardinale, Bradley J. Duffy, J. Emmett Gonzalez, Andrew Hooper, David U. Perrings, Charles Venail, Patrick Narwani, Anita Mace, Georgina M. Tilman, David Wardle, David A. Kinzig, Ann P. Daily, Gretchen C. Loreau, Michel Grace, James B. Larigauderie, Anne Srivastava, Diane S. Naeem, Shahid},
-author = {Cardinale, Bradley J. and Duffy, J. Emmett and Gonzalez, Andrew and Hooper, David U. and Perrings, Charles and Venail, Patrick and Narwani, Anita and Mace, Georgina M. and Tilman, David and Wardle, David A. and Kinzig, Ann P. and Daily, Gretchen C. and Loreau, Michel and Grace, James B. and Larigauderie, Anne and Srivastava, Diane S. and Naeem, Shahid},
-doi = {10.1038/nature11148},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cardinale et al. - 2012 - Biodiversity loss and its impact on humanity.pdf:pdf},
-journal = {Nature},
-number = {7401},
-pages = {59--67},
-title = {{Biodiversity loss and its impact on humanity}},
-volume = {486},
-year = {2012}
-}
-@unpublished{Laine1999,
-abstract = {La carte de l'emploi industriel reste contrast{\'{e}}e. Les effectifs sont importants au nord d'une diago- nale Nantes - Valence mais certaines industries ont une implantation sp{\'{e}}cifi- que li{\'{e}}e aux caract{\'{e}}ristiques du secteur. Les activit{\'{e}}s sont plus diversifi{\'{e}}es dans le Bassin parisien, les Pays de la Loire, en Alsace et dans le Sud-Est, tandis que les groupes et les grands {\'{e}}tablissements sont plus pr{\'{e}}sents dans le Nord et l'Est de la France. L'emploi industriel local est parfois contr{\^{o}}l{\'{e}} par quelques grands {\'{e}}ta- blissements, comme dans certains bas- sins isol{\'{e}}s et dans des zones d'implantation de l'industrie automobile. L'{\^{I}}le-de-France ainsi que les grandes m{\'{e}}tropoles du Sud b{\'{e}}n{\'{e}}ficient d'un niveau d'encadrement {\'{e}}lev{\'{e}}.},
-author = {Lain{\'{e}}, Fr{\'{e}}d{\'{e}}ric and Rieu, Carole},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lain{\'{e}}, Rieu - 1999 - La diversit{\'{e}} industrielle des territoires.pdf:pdf},
-isbn = {650},
-series = {Insee Premi{\`{e}}re},
-title = {{La diversit{\'{e}} industrielle des territoires}},
-url = {http://www.u-picardie.fr/CRIISEA/Docs{\_}DESS{\_}ERI/ip650.pdf},
-year = {1999}
-}
-@article{Mayr1966,
-author = {Mayr, Ernst},
-doi = {10.2307/sysbio/15.1.88a},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mayr - 1966 - The Proper Spelling of Taxonomy.pdf:pdf},
-journal = {Systematic Biology},
-month = {mar},
-number = {1},
-pages = {88--88},
-title = {{The Proper Spelling of Taxonomy}},
-url = {http://sysbio.oxfordjournals.org/cgi/doi/10.2307/sysbio/15.1.88a},
-volume = {15},
-year = {1966}
-}
-@article{Laxton1978,
-abstract = {The measure of diversity is developed from axiomatic foundations, independently of any statistical considerations, and various examples of such measures cited. It is shown that almost all the more usual measures which have been used in the past are closely related to measures which satisfy our axioms; thus the general theory of diversity is unified and comparisons between the various measures can be made. Brillouin's measure, which does satisfy our axioms, turns out to be the only one satisfying a further axiom. Shannon's function (from information theory) is shown to occupy a central position in our development as the asymptotic limit of average diversity measures. Finally we extend the notion of the measure to allow for various degrees of difference between classes in a set.},
-author = {Laxton, R.R.},
-doi = {10.1016/0022-5193(78)90302-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Laxton - 1978 - The measure of diversity.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-month = {jan},
-number = {1},
-pages = {51--67},
-title = {{The measure of diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/0022519378903028},
-volume = {70},
-year = {1978}
-}
-@article{Ricotta2017b,
-abstract = {The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.},
-author = {Ricotta, Carlo and Eszter, Ari and Bonanomi, Giuliano and Giannino, Francesco and Heathfield, Duncan and Mazzoleni, Stefano and Podani, Janos},
-doi = {10.1556/168.2017.18.1.5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2017 - Spatial analysis of phylogenetic community structure New version of a classical method.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {1--15},
-title = {{Spatial analysis of phylogenetic community structure: New version of a classical method}},
-url = {http://akademiai.com/doi/pdf/10.1556/168.2017.18.1.5},
-volume = {18},
-year = {2017}
-}
-@incollection{Openshaw1979,
-address = {London},
-author = {Openshaw, S. and Taylor, P. J.},
-booktitle = {Statistical Applications in the Spatial Sciences},
-editor = {Wrigley, N},
-pages = {127--144},
-publisher = {Pion},
-title = {{A million or so correlation coefficients: three experiments on the modifiable areal unit problem}},
-year = {1979}
-}
-@article{Lavorel2013,
-abstract = {A novel conceptual framework is presented that proposes to apply trait-based approaches to predicting the impact of environmental change on ecosystemser- vice delivery by multi-trophic systems. Development of the framework was based on an extension of the response–effect trait approach to capture functional relationships that drive trophic interactions. The frameworkwas populated with worked examples to demonstrate its flexibility and value for linking disparate data sources, identifying knowledge gaps and generating hypotheses for quanti- tativemodels.},
-author = {Lavorel, Sandra and Storkey, Jonathan and Bardgett, Richard D. and {De Bello}, Francesco and Berg, Matty P. and {Le Roux}, Xavier and Moretti, Marco and Mulder, Christian and Pakeman, Robin J. and D{\'{i}}az, Sandra and Harrington, Richard},
-doi = {10.1111/jvs.12083},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lavorel et al. - 2013 - A novel framework for linking functional diversity of plants with other trophic levels for the quantification of.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {942--948},
-title = {{A novel framework for linking functional diversity of plants with other trophic levels for the quantification of ecosystem services}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/jvs.12083/abstract},
-volume = {24},
-year = {2013}
-}
-@article{Hanberry2013,
-abstract = {Three functions that analyze point patterns are the L (a transformation of Ripley's K function), pair correlation, and K2 functions. We tested these functions with Genton's spatial index, which measures the distance between observed and random theoretical lines for a function over all lag distances. We simulated points from random, moderately regular, extremely regular, and clustered distributions at different density levels and a fixed plot size and for regular distributions at varying plot sizes. The spatial index clearly was able to identify clustered patterns. However, there was overlap in spatial index values between random and moderately regular distributions at lower densities. The spatial index for the L function also became more negative as plot size increased, indicating edge effects, whereas the pair correlation and K2 function values fluctuated with plot size. Using confidence envelopes rather than a spatial index, we also identified distributions other than the known distribution at low densities. These results indicate that ecologists should be cautious about 1) assigning random or regular distribution, particularly for the L function and the K2 function, 2) comparing point patterns of different densities and plot sizes, and 3) interpreting the pair correlation and K2 functions.},
-author = {Hanberry, B. B. and Yang, Jian and He, Hong S.},
-doi = {10.1556/ComEc.14.2013.1.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hanberry, Yang, He - 2013 - Evaluating functions to describe point patterns.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {1--7},
-title = {{Evaluating functions to describe point patterns}},
-url = {http://dx.doi.org/10.1556/ComEc.14.2013.1.1},
-volume = {14},
-year = {2013}
-}
-@article{Fule1998,
-abstract = {Patterns of spatial arrangement, tree density, and species composition were compared in three unharvested pine-oak forests under different recent fire regimes: (1) an uninterrupted frequent fire regime, (2) fire exclusion, and (3) fire exclusion followed by the return of fire. Regeneration was dense and highly aggregated at all sites but the frequent-fire overstory was random to uniform in spatial distribution and relatively open while the fire-excluded sites had clumped overstory trees with a high density of smaller trees. Dominance by sprouting species was greatest at the fire-excluded sites. Mortality was spatially aggregated at all sites, consistent both with thinning by fire and density-dependent mortality, but competitive self-thinning appeared insufficient to counteract the increased tree density without fire. The return of fire after 29 years of exclusion reduced tree density but left overstory trees aggregated and led to vigorous oak and alder sprouting. Frequent fire disturbance is considered essential to maintain open pine forests; fire exclusion with or without subsequent fire appears to lead to denser forests dominated by smaller trees of sprouting species.},
-author = {Ful{\'{e}}, Peter Z. and Covington, W. Wallace},
-doi = {10.1023/A:1009789018557},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ful{\'{e}}, Covington - 1998 - Spatial patterns of Mexican pine-oak forests under different recent fire regimes.pdf:pdf},
-journal = {Plant Ecology},
-pages = {197--209},
-title = {{Spatial patterns of Mexican pine-oak forests under different recent fire regimes}},
-url = {https://link.springer.com/article/10.1023/A:1009789018557},
-volume = {134},
-year = {1998}
-}
-@article{Pechackova1999,
-abstract = {1 We investigated the fine-scale below-ground distribution of plant parts in a mountain grassland. Roots and rhizomes were identified to the species level by tracking their connections to above-ground parts. 2 Fine-scale horizontal heterogeneity of total root and rhizome biomass at different depths was recorded at the same time in the same grassland. 3 Both pairwise and multivariate statistical analysis showed that in the 0-3 cm layer the frequencies of roots and rhizomes of individual plants were closely coupled to the occurrence of the same species immediately above-ground. In contrast, in the 3-6 cm layer, these correlations peaked when root and rhizome frequencies were compared with plants above-ground displaced by a horizontal distance of 2 cm. This confirms the predominantly inclined growth of both roots and rhizomes; while the inclined growth has been shown regularly by studying single plants, the current study shows its prevalence at the community level as well. 4 The similarity to the above-ground patterns in the upper soil layer was due to the spatial constraints of plant presence above-ground; in contrast, the spatial patterns in the 3-6 cm layer were independent of plant presence above-ground. The role of root growth plasticity is discussed in this context. 5 Autocorrelation analysis of the root data revealed that there was a pronounced difference in the grain of horizontal spatial pattern between total root biomass and species-specific root frequencies. All the species had rather loose root systems and clumps of one species rarely extended more than 0.5cm. In contrast, there was significant long-range clumping of root biomass up to 10 cm. The below-ground heterogeneities in overall biomass and in species-specific distributions were therefore probably determined by different environmental processes. 6 No such difference in clumping range between total biomass and species-specific frequencies was observed in above-ground parts. This was attributed to homogeneity of the above-ground resource (light) compared with the inherently heterogeneous nature of the below-ground resources, and the different nature of competition for these resources may account for differences in vegetation patterns above- and below-ground.},
-author = {Pechackova, Sylvie and During, Heinjo J. and Rydlova, Vera and Herben, Tomas},
-doi = {10.1046/j.1365-2745.1999.00375.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pechackova et al. - 1999 - Species-Specific Spatial Pattern of Below-Ground Plant Parts in a Montane Grassland Community.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {569--582},
-title = {{Species-Specific Spatial Pattern of Below-Ground Plant Parts in a Montane Grassland Community}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2745.1999.00375.x/abstract},
-volume = {87},
-year = {1999}
-}
-@article{Peyrard2005,
-abstract = {Les tests de permutation font r{\'{e}}f{\'{e}}rence {\`{a}} des m{\'{e}}thodes pour l'exploration d'un jeu de donn{\'{e}}es sans hypoth{\`{e}}se sur leur distribution. Ces m{\'{e}}thodes, simples {\`{a}} mettre en oeuvre, permettent de mettre en {\'{e}}vidence des caract{\'{e}}ristiques sous-jacentes aux donn{\'{e}}es, que l'on pourra vouloir traduire dans un mod{\`{e}}le dans une seconde {\'{e}}tape d'analyse plus fine. Ce type de tests est largement utilis{\'{e}} dans le cas d'observations ind{\'{e}}pendantes. Dans le cadre de donn{\'{e}}es observ{\'{e}}es sur grille, la mise en {\'{e}}vidence de la structure spatiale des donn{\'{e}}es conduit {\`{a}} un ensemble de tests sp{\'{e}}cifiques. Nous pr{\'{e}}sentons ainsi dans cet article comment aborder la v{\'{e}}rification d'un certain nombre d'hypoth{\`{e}}ses classiques au cas spatial dans le cadre des tests de permutation.},
-author = {Peyrard, N. and Calonnec, Agn{\`{e}}s and Bonnot, Fran{\c{c}}ois and Chadoeuf, Jo{\"{e}}l},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peyrard et al. - 2005 - Explorer un jeu de donn{\'{e}}es sur grille par tests de permutation.pdf:pdf},
-journal = {Revue de Statistique Appliqu{\'{e}}e},
-number = {1},
-pages = {59--78},
-title = {{Explorer un jeu de donn{\'{e}}es sur grille par tests de permutation}},
-volume = {53},
-year = {2005}
-}
-@techreport{Haaland1999,
-author = {Haaland, Jan I. and Kind, Hans Jarle and Midelfart-Knarvik, Karen Helene and Torstensson, Johan},
-isbn = {2072},
-keywords = {Haaland (1999).pdf},
-mendeley-tags = {Haaland (1999).pdf},
-publisher = {Centre for Economic Policy Research},
-title = {{What determines the economic geography of Europe?}},
-year = {1999}
-}
-@article{Grime1998,
-abstract = {1 It is useful to distinguish between the immediate effects of species richness on ecosystems and those which become apparent on a longer time scale, described here as filter and founder effects. 2 Relationships between plant diversity and ecosystem properties can be explored by classifying component species into three categories - dominants, subordinates and transients. Dominants recur in particular vegetation types, are relatively large, exhibit coarse-grained foraging for resources and, as individual species, make a substantial contribution to the plant biomass. Subordinates also show high fidelity of association with particular vegetation types but they are smaller in stature, forage on a more restricted scale and tend to occupy microhabitats delimited by the architecture and phenology of their associated dominants. Transients comprise a heterogeneous assortment of species of low abundance and persistence: a high proportion are juveniles of species that occur as dominants or subordinates in neighbouring ecosystems. 3 A 'mass ratio' theory proposes that immediate controls are in proportion to inputs to primary production, are determined to an overwhelming extent by the traits and functional diversity of the dominant plants and are relatively insensitive to the richness of subordinates and transients. Recent experiments support the mass ratio hypothesis and the conclusion of Huston (1997) that claims of immediate benefits of high species richness to ecosystem functions arise from misinterpretation of data. 4 Attribution of immediate control to dominants does not exclude subordinates and transients from involvement in the determination of ecosystem function and sustainability. Both are suspected to play a crucial, if intermittent, role by influencing the recruitment of dominants. Some subordinates may act as a filter influencing regeneration by dominants following major perturbations. 5 Transients originate from the seed rain and seed banks and provide an index of the pool of potential dominants and subordinates at specific sites. Where the landscape carousel operates against a background of declining diversity in the reservoir of colonizing transients, we may predict that a progressive loss of ecosystem functions will arise from the decline in the precision with which dominants can engage in the re-assembly and relocation of ecosystems},
-author = {Grime, J. P.},
-doi = {10.1046/j.1365-2745.1998.00306.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grime - 1998 - Benefits of plant diversity to ecosystems Immediate, filter and founder effects.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {902--910},
-title = {{Benefits of plant diversity to ecosystems: Immediate, filter and founder effects}},
-url = {http://www.jstor.org/stable/2648655},
-volume = {86},
-year = {1998}
-}
-@article{Baraloto2012,
-abstract = {1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and we integrated a database of 13 functional traits describing leaf and wood economics of tropical trees. 3. We found no differences in taxonomic and functional richness among habitats, but logging gaps had significantly higher taxonomic and functional evenness. 4. Logging also effected striking, long-term changes in both species and functional composition. In particular, the xylem density of recruits in logging gaps was 6{\%} less than in unlogged forests, leaves were 11{\%}less tough and had 6–13{\%}greater mineral nutrient concentrations. 5. Synthesis and applications. Our results suggest that managers of tropical forests should limit overall surface area converted to logging gaps by creating fewer, larger gaps during selective logging, to reduce impacts on the taxonomic and functional composition of the regenerating stand.},
-author = {Baraloto, Christopher and H{\'{e}}rault, Bruno and Paine, C. E. Timothy and Massot, H{\'{e}}l{\`{e}}ne and Blanc, Lilian and Bonal, Damien and Molino, Jean-Fran{\c{c}}ois and Nicolini, Eric A. and Sabatier, Daniel},
-doi = {10.1111/j.1365-2664.2012.02164.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2012 - Contrasting taxonomic and functional responses of a tropical tree community to selective logging.pdf:pdf},
-journal = {Journal of Applied Ecology},
-number = {4},
-pages = {861--870},
-title = {{Contrasting taxonomic and functional responses of a tropical tree community to selective logging}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2664.2012.02164.x/abstract},
-volume = {49},
-year = {2012}
-}
-@techreport{Autant-Bernard1999a,
-address = {Saint-Etienne, France},
-author = {Autant-Bernard, Corinne},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Autant-Bernard - 1999 - G{\'{e}}ographie des externalit{\'{e}}s de connaissance et proximit{\'{e}} technologiques.pdf:pdf},
-keywords = {Autant-Bernard (1999).pdf},
-mendeley-tags = {Autant-Bernard (1999).pdf},
-publisher = {Centre de Recherches Economiques de l'Universit{\'{e}} de Saint-Etienne},
-title = {{G{\'{e}}ographie des externalit{\'{e}}s de connaissance et proximit{\'{e}} technologiques}},
-year = {1999}
-}
-@article{Marcon2012a,
-abstract = {Beta diversity is among the most employed theoretical concepts in ecology and biodiversity conservation. Up to date, a self-contained definition of it, with no reference to alpha and gamma diversity, has never been proposed. Using Kullback-Leibler divergence, we present the explicit formula of Shannon's $\beta$ entropy, a bias correction for its estimator and a confidence interval. We also provide the mathematical framework to decompose Shannon diversity into several hierarchical nested levels. From botanical inventories of tropical forest plots in French Guiana, we estimate Shannon diversity at the plot, forest and regional level. We believe this is a complete and usefulness toolbox for ecologists interested in partitioning biodiversity.},
-author = {Marcon, Eric and H{\'{e}}rault, Bruno and Baraloto, Christopher and Lang, Gabriel},
-doi = {10.1111/j.1600-0706.2011.19267.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon et al. - 2012 - The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity.pdf:pdf},
-journal = {Oikos},
-number = {4},
-pages = {516--522},
-title = {{The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2011.19267.x/abstract},
-volume = {121},
-year = {2012}
-}
-@book{Holdridge1971,
-address = {Oxford},
-author = {Holdridge, L. R. and Grenke, W. C. and Hatheway, W. H. and Liang, T. and Tosi, J. A.},
-publisher = {Pergamon Press},
-title = {{Forest environments in tropical life zones}},
-year = {1971}
-}
-@article{Carmona2012,
-abstract = {Changes in livestock grazing regimes are among the most important drivers of species loss and decrease in functional diversity world-wide. However, taxonomic and functional diversities (TD and FD) can respond differently to changes in grazing regime or productivity. 2. We surveyed plant communities from 67 sites under different grazing regimes (from heavy grazing to grazing abandonment) in wet and dry habitats, in both wet and dry years. We tested the influence of grazing intensity, habitat type and rainfall on TD, FD and the relationship between them. We also partitioned diversity to examine the effects of grazing on TD and FD across scales (within communities, within grazing levels and between grazing levels). 3. The effect of grazing within and across communities was modulated by water availability, with grazing showing the strongest effects in dry habitats. The relationship between FD and TD varied between habitat types and years and revealed high functional similarity between species (i.e. redundancy) in dry habitats. TD was reduced in the driest conditions across all the observation levels, contrasting with the high temporal stability of FD, suggesting that FD was decoupled from TD, especially in dry habitats. However, despite the high temporal and spatial stability of FD, results show that under severely limited water availability, high grazing pressure can reduce FD, revealing a convergence in traits under the combined effect of grazing and drought conditions. 4. Synthesis and applications. Results highlight the dependence of functional diversity on the combined effect of water availability and grazing regime. Under severely limited water availability, grazing intensification reduced the functional diversity of these grasslands. Because of the foreseeable reduction in water availability in Mediterranean environments, we recommend the adoption of flexible grazing management schemes that take species and functional diversities into account simultaneously and adapt the level of grazing pressure to water availability.},
-author = {Carmona, Carlos P. and Azc{\'{a}}rate, Francisco M. and de Bello, Francesco and Ollero, Helios S. and Lep{\v{s}}, Jan and Peco, Bego{\~{n}}a},
-doi = {10.1111/j.1365-2664.2012.02193.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carmona et al. - 2012 - Taxonomical and functional diversity turnover in Mediterranean grasslands Interactions between grazing, habitat.pdf:pdf},
-journal = {Journal of Applied Ecology},
-number = {5},
-pages = {1084--1093},
-title = {{Taxonomical and functional diversity turnover in Mediterranean grasslands: Interactions between grazing, habitat type and rainfall}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2664.2012.02193.x/abstract},
-volume = {49},
-year = {2012}
-}
-@article{Sonnier2010,
-abstract = {Questions: To what extent can Shipley et al.'s original maximum entropy model of trait-based community assembly predict relative abundances of species over a large (3000km2) landscape?How does variation in the species pool affect predictive ability of the model? Howmight the effects of missing traits be detected? How can non-trait-based processes be incorporated into the model? Location: Central England. Material andMethods: Using 10 traits measured on 506 plant species from 1308 1-m2 plots collected over 3000km2 in central England, we tested one aspect of Shipley et al.'s original maximum entropy model of ‘‘pure'' trait-based community assembly (S1), and modified it to represent both a neutral (S2) and a hybrid (S3) scenario of community assembly at the local level. Predictive ability of the three corresponding models was determined with differ- ent species pool sizes (30, 60, 100 and 506 species). Statistical significance was tested using a distribu- tion-free permutation test. Results: Predictive ability was high and significantly different from random expectations in S1. Predictive ability was low but significant in S2. Highest pre- dictive ability occurred when both neutral and trait- based processes were included in the model (S3). Increasing the pool size decreased predictive ability, but less so in S3. Incorporating habitat affinity (to indicate missing traits) increased predictive ability. Conclusions: The measured functional traits were significantly related to species relative abundance. Our results both confirm the generality of the original model but also highlight the importance of (i) taking into account neutral processes during assembly of a plant community, and (ii) properly defining the species pool. Sonnier,},
-author = {Sonnier, Gr{\'{e}}gory and Shipley, Bill and Navas, Marie-Laure},
-doi = {10.1111/j.1654-1103.2009.01145.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sonnier, Shipley, Navas - 2010 - Plant traits, species pools and the prediction of relative abundance in plant communities a maximum ent.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {318--331},
-title = {{Plant traits, species pools and the prediction of relative abundance in plant communities: a maximum entropy approach}},
-volume = {21},
-year = {2010}
-}
-@article{Ricotta2015a,
-abstract = {Aims: The identification of diagnostic or indicator species with high fidelity to a given group of sites is an important step for the ecological characterization of habitats or community types. The determination of the degree of fidelity to a target group is traditionally performed by analysing the concentration of species occurrences or abundances in different groups of sites. Surprisingly, although one of the main purposes of indicator species analysis is to give ecological meaning to groups of sites, none of the methods proposed to date take into account the functional ecology of diagnostic species. Therefore, the question we address here is: can we use functional traits of species to improve the diagnostic value of indicator species? Location: Sand dune communities in central Italy. Methods: In this paper we propose a two-step procedure for incorporating the functional traits of a given species in the evaluation of its diagnostic value. For a given set of plots that are classified into different groups, first the indicator species that best characterize each group of plots are identified with the usual statistical tools based on species occurrences. Next, the functional association between the indicator species and the target groups of plots is tested bymeasuring the functional distance between the indicator species and the centroids of all plots in the target group. A species is positively associated with a group if its mean functional distance from all plot centroids in the group is significantly lower than expected. Results: In this example, we show that the functional association of the indicator species with a given habitat type is represented by less species than the association highlighted solely through species occurrences and/or abundances. This subset of species appears to better characterize the functional ecology of coastal dune plant assemblages and shows a higher diagnostic value in comparison with those obtained through the traditional indicator analysis. Conclusions: As functional traits are the main ecological attributes by which different species influence ecosystem processes, we believe that the methodology proposed here provides a relevant tool for ecological applications as distinct as vegetation science, conservation biology or landscapemanagement.},
-author = {Ricotta, Carlo and Carboni, Marta and Acosta, Alicia T.R.},
-doi = {10.1111/jvs.12291},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Carboni, Acosta - 2015 - Let the concept of indicator species be functional!.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {1},
-pages = {839--847},
-title = {{Let the concept of indicator species be functional!}},
-url = {http://doi.wiley.com/10.1111/jvs.12291},
-volume = {5},
-year = {2015}
-}
-@article{Schenk2003,
-abstract = {1 Spatial pattern analyses were used to generate hypotheses about the processes that shape the structure of a plant community in the Mojave Desert of North America, with a focus on the semi-shrub Ambrosia dumosa. We analysed spatial distributions and sizes of this species relative to other semi-shrubs, shrubs and annuals, and the relationships between spatial patterns and abiotic and biotic habitat characteristics. 2 The analyses were based on maps of sample plots placed along a transect spanning two adjacent geological substrates: aeolian sand and gravelly, sandy to loamy alluvium. Of these two substrates, sand supported higher total biomasses of Ambrosia and of all woody perennials, while alluvium supported on average higher biomasses of winter annuals. 3 Annuals and seedlings of Ambrosia were much more strongly aggregated with Ambrosia canopies on sand than on alluvium, suggesting that these small plants were more strongly facilitated by Ambrosia on sand than on alluvium. 4 Ambrosia semi-shrubs were spatially segregated on sand but aggregated on alluvium, and the degree of segregation on sand increased with the total above-ground biomass of Ambrosia per unit area, indicating that negative interactions between Ambrosia plants were stronger in more productive habitats. Canopy sizes of Ambrosia in all mapped plots increased with distance to the nearest conspecific neighbour, which suggests that neighbour interactions negatively affected plant sizes. 5 Ambrosia plants on sand were spatially aggregated with Acamptopappus sphaerocephalus semi-shrubs, suggesting that at least one of these species may benefit from the association. Ambrosia plants were spatially segregated from Larrea tridentata shrubs on both substrates, possibly due to negative effects of Larrea roots on Ambrosia roots reported in previous studies. 6 Subtle differences in substrate characteristics were correlated with strong differences in the spatial distribution of Ambrosia plants relative to their neighbours, which suggests that edaphic conditions may affect the spatial structure of the community by modifying complex positive and negative interactions between neighbouring plants.},
-author = {Schenk, H. Jochen and Holzapfel, Claus and Hamilton, Jason G. and Mahall, Bruce E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schenk et al. - 2003 - Spatial ecology of a small desert shrub on adjacent geological substrates.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {383--395},
-title = {{Spatial ecology of a small desert shrub on adjacent geological substrates}},
-url = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2745.2003.00782.x/abs},
-volume = {91},
-year = {2003}
-}
-@article{Ratnayake1999,
-author = {Ratnayake, Ravi},
-journal = {International Journal of Industrial Organization},
-pages = {1041--1057},
-title = {{Industry concentration and competition: New Zealand experience}},
-volume = {17},
-year = {1999}
-}
-@article{Jost2006,
-abstract = {Entropies such as the Shannon–Wiener and Gini–Simpson indices are not themselves diversities. Conversion of these to effective number of species is the key to a unified and intuitive interpretation of diversity. Effective numbers of species derived from standard diversity indices share a common set of intuitive mathematical properties and behave as one would expect of a diversity, while raw indices do not. Contrary to Keylock, the lack of concavity of effective numbers of species is irrelevant as long as they are used as transformations of concave alpha, beta, and gamma entropies. The practical importance of this transformation is demonstrated by applying it to a popular community similarity measure based on raw diversity indices or entropies. The standard similarity measure based on untransformed indices is shown to give misleading results, but transforming the indices or entropies to effective numbers of species produces a stable, easily interpreted, sensitive general similarity measure. General overlap measures derived from this transformed similarity measure yield the Jaccard index, S{\o}rensen index, Horn index of overlap, and the Morisita–Horn index as special cases.},
-author = {Jost, Lou},
-doi = {10.1111/j.2006.0030-1299.14714.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2006 - Entropy and diversity.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {363--375},
-title = {{Entropy and diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.2006.0030-1299.14714.x/abstract},
-volume = {113},
-year = {2006}
-}
-@article{Wiegand1998,
-abstract = {We used auto- and cross-correlation analysis and Ripley's K-function analysis to analyze spatiotemporal pattern evolution in a spatially explicit simulation model of a semiarid shrubland (Karoo, South Africa) and to determine the impact of small-scale disturbances on system dynamics. Without disturbance, local dynamics were driven by a pattern of cyclic succession, where "colonizer" and "successor" species alternately replaced each other. This results in a strong pattern of negative correlation in the temporal distribution of colonizer and successor species. As disturbance rates were increased, the relationship shifted from being negatively correlated in time to being positively correlated-the dynamics became decoupled from the ecologically driven cyclic succession and were increasingly influenced by abiotic factors (e.g., rainfall events). Further analysis of the spatial relationships among colonizer and successor species showed that, without disturbance, periods of attraction and repulsion between colonizer and successor species alternate cyclically at intermediate spatial scales. This was due to the spatial "memory" embedded in the system through the process of cyclic succession. With the addition of disturbance, this pattern breaks down, although there is some indication of increasing ecological organization at broader spatial scales. We suggest that many of the insights that can be gained through spatially explicit models will only be obtained through a direct analysis of the spatial patterns produced.},
-annote = {Article
-English
-AMER NATURALIST
-110NP},
-author = {Wiegand, Thorsten and Moloney, Kirk A. and Milton, Suzanne J.},
-doi = {10.1086/286172},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand, Moloney, Milton - 1998 - Population dynamics, disturbance, and pattern evolution Identifying the fundamental scales of organiza.pdf:pdf},
-journal = {The American Naturalist},
-number = {3},
-pages = {321--337},
-title = {{Population dynamics, disturbance, and pattern evolution: Identifying the fundamental scales of organization in a model ecosystem}},
-url = {http://www.jstor.org/stable/10.1086/286172},
-volume = {152},
-year = {1998}
-}
-@article{Quigley1998,
-author = {Quigley, John M},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Quigley - 1998 - Urban Diversity and Economic Growth.pdf:pdf},
-journal = {Journal of Economic Perspectives},
-number = {2},
-pages = {127--138},
-title = {{Urban Diversity and Economic Growth}},
-volume = {12},
-year = {1998}
-}
-@article{Corona2015,
-abstract = {A number of international agreements and commitments emphasize the importance of appropriate monitoring protocols and assessments as prerequisites for sound conservation and management of the world's forest ecosystems. Mandated periodic surveys, like forest inventories, provide a unique opportunity to identify and properly satisfy natural resource management information needs. Distinctively, there is an increasing need for detecting diversity by means of unambiguous diversity measures. Because all diversity measures are functions of tree species abundances, estimation of tree diversity indices and profiles is inevitably performed by estimating tree species abundances and then estimating indices and profiles as functions of the abundance estimates. This strategy can be readily implemented in the framework of current forest inventory approaches, where tree species abundances are routinely estimated by means of plots placed onto the surveyed area in accordance with probabilistic schemes. The purpose of this paper is to assess the effectiveness of this strategy by reviewing the- oretical results from published case studies. Under uniform random sampling (URS), that is when plots are uniformly and independently located on the study region, con- sistency and asymptotic normality of diversity index estimators follow from standard limit theorems as the sampling effort increases. In addition, variance estimation and bias reduction are achieved using the jackknife method. Despite its theoretical simplicity, URS may lead to uneven coverage of the study region. In order to avoid unbalanced sampling, the use of tessellation stratified sampling (TSS) is suggested. TSS involves covering the study region by a polygonal grid and randomly selecting a plot in each polygon. Under TSS, the diversity index estimators are consistent, asymptotically normal and more precise than those achieved using URS. Variance estimation is pos- sible and there is no need to reduce bias.},
-author = {Corona, Piermaria and Franceschi, Sara and Pisani, Caterina and Portoghesi, Luigi and Mattioli, Walter and Fattorini, Lorenzo},
-doi = {10.1007/s10531-015-1017-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Corona et al. - 2015 - Inference on diversity from forest inventories a review.pdf:pdf},
-journal = {Biodiversity and Conservation},
-title = {{Inference on diversity from forest inventories: a review}},
-url = {http://link.springer.com/article/10.1007/s10531-015-1017-2},
-volume = {in press},
-year = {2015}
-}
-@article{Peres-Neto2006,
-abstract = {Establishing relationships between species distributions and environmental characteristics is a major goal in the search for forces driving species distributions. Canonical ordinations such as redundancy analysis and canonical correspondence analysis are invaluable tools for modeling communities through environmental predictors. They provide the means for conducting direct explanatory analysis in which the association among species can be studied according to their common and unique relationships with the environmental variables and other sets of predictors of interest, such as spatial variables. Variation partitioning can then be used to test and determine the likelihood of these sets of predictors in explaining patterns in community structure. Although variation partitioning in canonical analysis is routinely used in ecological analysis, no effort has been reported in the literature to consider appropriate estimators so that comparisons between fractions or, eventually, between different canonical models are meaningful. In this paper, we show that variation partitioning as currently applied in canonical analysis is biased. We present appropriate unbiased estimators. In addition, we outline a statistical test to compare fractions in canonical analysis. The question addressed by the test is whether two fractions of variation are significantly different from each other. Such assessment provides an important step toward attaining an understanding of the factors patterning community structure. The test is shown to have correct Type I error rates and good power for both redundancy analysis and canonical correspondence analysis.},
-archivePrefix = {arXiv},
-arxivId = {2655},
-author = {Peres-Neto, Pedro R. and Legendre, Pierre and Dray, St{\'{e}}phane and Borcard, Daniel},
-doi = {10.1890/0012-9658(2006)87[2614:VPOSDM]2.0.CO;2},
-eprint = {2655},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peres-Neto et al. - 2006 - Variation partitioning of species data matrices Estimation and comparison of fractions.pdf:pdf},
-journal = {Ecology},
-number = {10},
-pages = {2614--2625},
-title = {{Variation partitioning of species data matrices: Estimation and comparison of fractions}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12425/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Ollivier2007,
-abstract = {We present a plant trait database covering autecology for rain forest trees of French Guiana. The database comprises more than thirty traits including autecology (e.g., habitat associations and reproductive phenology), wood structure (e.g., density and tension characteristics) and physiology at the whole plant (e.g., carbon and nitrogen isotopes) and leaf level (e.g., specific leaf area, photosynthetic capacity). The current database describes traits for about nine hundred species from three hundred genera in one hundred families. For more than sixty species, data on twelve morphological and ecophysiological traits are provided for individual plants under different environmental conditions and at different ontogenetic stages. The database is thus unique in permitting intraspecific analyses, such as the effects of ontogenetic stages or environmental conditions on trait values and their relationships.},
-author = {Ollivier, Mariwenn and Baraloto, Christopher and Marcon, Eric},
-doi = {10.1051/forest:2007058},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ollivier, Baraloto, Marcon - 2007 - A trait database for Guianan rain forest trees permits intra- and inter-specific contrasts.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {7},
-pages = {781--786},
-title = {{A trait database for Guianan rain forest trees permits intra- and inter-specific contrasts}},
-url = {http://www.afs-journal.org/articles/forest/abs/2007/07/f7081/f7081.html},
-volume = {64},
-year = {2007}
-}
-@article{RICHARDS1969,
-abstract = {early paper, reference paper - introducing niche concepts into debate on rainforest species diversity},
-author = {Richards, P. W.},
-doi = {10.1111/j.1095-8312.1969.tb01817.x},
-isbn = {Niche},
-issn = {10958312},
-journal = {Biological Journal of the Linnean Society},
-number = {1-2},
-pages = {149--153},
-title = {{Speciation in the tropical rain forest and the concept of the niche}},
-volume = {1},
-year = {1969}
-}
-@article{Gini1955,
-author = {Gini, Corrado},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gini - 1955 - Sur quelques questions fondamentales de statistique.pdf:pdf},
-journal = {Annales de l'I.H.P.},
-number = {4},
-pages = {245--364},
-title = {{Sur quelques questions fondamentales de statistique}},
-url = {http://www.numdam.org/item/AIHP{\_}1955{\_}{\_}14{\_}4{\_}245{\_}0},
-volume = {14},
-year = {1955}
-}
-@incollection{Feser2002a,
-abstract = {Recent theoretical work in the so-called new economic geography echoes early agglomeration theory in its focus on spatial externalities as a key driver of the geographic concentration of industry. But businesses cluster in space for a variety of reasons in addition to externalities or agglomeration economies, including to access natural resources, to take advantage of existing transportation networks (canals, harbors, rail, roads and airports), and to comply with land use regulations or zoning restrictions. The wide range of possible factors behind observed clustering patterns makes empirical research on spatial externalities difficult. We begin the paper by briefly reviewing the existing theoretical and empirical research on business clustering, focusing particular attention on major differences across disciplines (regional science, economics, and geography). We then describe and implement a new approach to detecting hypothesized sources of business clustering from an analysis of observed patterns of business locations: the use of point process models in conjunction with a case-control research design. Specifically, we show how it is possible to isolate the role of specific and commonly cited factors behind clustering–in this case, presence in a common product value chain–from other influences on spatial concentration. In an analysis of multiple manufacturing value chains across fourteen metropolitan areas, we find considerable variation in the results: some value chains are only infrequently clustered (suggesting the absence of externalities or agglomeration economies) while others often clustered. In a concluding section to the chapter, we discuss the implications of the findings and suggest next steps in this line of research.},
-address = {Cheltenham},
-author = {Feser, Edward J. and Sweeney, Stuart H.},
-booktitle = {Industrial Location Economics},
-editor = {McCann, P},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser, Sweeney - 2002 - Theory, methods, and a cross-metropolitan comparison of business clustering.pdf:pdf},
-pages = {222--257},
-publisher = {Edward Elgar},
-title = {{Theory, methods, and a cross-metropolitan comparison of business clustering}},
-url = {http://www.planning.unc.edu/facstaff/faculty/feserDocs.htm},
-year = {2002}
-}
-@article{Smith2008,
-abstract = {Question: How can species–area relationships (SPARs) be studied in biotas where only data from isolated localities are available? Data: The Breeding Bird Survey at a spatial scale of 102 –103 km. Analytic methods: I develop a method that involves numeric estimation of the shortest path connecting a set of localities and calculation of cumulative species richness (corrected for sample size) and distance along that path. The slope of the resulting species–distance relationship (SDR) is used as a measure of beta diversity. Results: The slope of the SDR is insensitive to locality area and to inter-locality distance at the scales considered. It is, however, sensitive to the number of specimens per locality; in particular, the slope of the SDR declines as more specimens are included and is lowest when incidence data are used (i.e. all the specimens are included). The slope of the SDR is strongly correlated with and numerically similar to that of a corresponding SPAR. The slope of the relation between distance and similarity (measured as the Jaccard or S{\o}rensen index) is also positively, but less strongly, correlated with the slope of the SPAR for these data. Conclusions: The SDR is an analog for point sources of the SPAR. It estimates the SPAR slope more accurately than similarity metrics and sometimes just as precisely.},
-author = {Smith, Krister T.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith - 2008 - On the measurement of beta diversity an analog of the species-area relationship for point sources.pdf:pdf},
-journal = {Evolutionary Ecology Research},
-number = {7},
-pages = {987--1006},
-title = {{On the measurement of beta diversity: an analog of the species-area relationship for point sources}},
-volume = {10},
-year = {2008}
-}
-@article{Taudiere2016,
-abstract = {Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null-model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses. Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T-statistics. More generally, the cati package 1) calculates a variety of single-trait and multi-trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non-random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions. The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.},
-author = {Taudi{\`{e}}re, Adrien and Violle, Cyrille},
-doi = {10.1111/ecog.01433},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Taudi{\`{e}}re, Violle - 2016 - cati an R package using functional traits to detect and quantify multi-level community assembly processes.pdf:pdf},
-journal = {Ecography},
-number = {7},
-pages = {699--708},
-title = {{cati: an R package using functional traits to detect and quantify multi-level community assembly processes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.01433/abstract},
-volume = {39},
-year = {2016}
-}
-@article{Nehring2002,
-abstract = {How can diversity be measured? What does it mean to value biodiversity? Can we assist Noah in constructing his preferences? To address these questions, we propose a multi-attribute approach under which the diversity of a set of species is the sum of the values of all attributes possessed by some species in the set. We develop the basic intuitions and requirements for a theory of diversity and show that the multi-attribute approach satisfies them in a flexible yet tractable manner. A natural starting point is to think of the diversity of a set as an aggregate of the pairwise dissimilarities between its elements. The multi-attribute framework allows one to make this program formally precise. It is shown that the program can be realized if and only if the family of relevant attributes is well-ordered (“acyclic”). Moreover, there is a unique functional form aggregating dissimilarity into diversity, the length of a minimum spanning tree. Examples are taxonomic hierarchies and lines representing uni-dimensional qualities. In multi-dimensional settings, pairwise dissimilarity information among elements is insufficient to determine their diversity. By consequence, the qualitative and quantitative behavior of diversity differs fundamentally.},
-author = {Nehring, Klaus and Puppe, Clemens},
-doi = {10.1111/1468-0262.00321},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nehring, Puppe - 2002 - A Theory of Diversity.pdf:pdf},
-journal = {Econometrica},
-number = {3},
-pages = {1155--1198},
-title = {{A Theory of Diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1468-0262.00321/full},
-volume = {70},
-year = {2002}
-}
-@article{Guimaraes2009,
-abstract = {In this paper we reinterpret the location quotient, the commonly employed measure of regional industrial agglomeration, as an estimator derived from Ellison and Glaeser [Ellison, G., and Glaeser, E., 1997. Geographic concentration in U.S. manufacturing industries: a dartboard approach. Journal of Political Economy 105 (5), 889-927.] dartboard framework. This approach provides a theoretical foundation on which to build statistical tests for the measure. With a simple application, we show that these tests provide valuable information about the accuracy of the location quotient. The tests are relatively easy to implement using regional employment and establishment data. {\textcopyright} 2009 Elsevier B.V. All rights reserved.},
-author = {Guimar{\~{a}}es, Paulo and Figueiredo, Oct{\'{a}}vio and Woodward, Douglas},
-doi = {10.1016/j.regsciurbeco.2008.12.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guimar{\~{a}}es, Figueiredo, Woodward - 2009 - Dartboard tests for the location quotient.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {3},
-pages = {360--364},
-title = {{Dartboard tests for the location quotient}},
-url = {http://dx.doi.org/10.1016/j.regsciurbeco.2008.12.003},
-volume = {39},
-year = {2009}
-}
-@article{Hoffmann2005,
-abstract = {1. Leaf traits are commonly associated with the life history, distribution and resource requirements of a species. To improve our understanding of the ecological and physiological differences between tropical savanna and forest trees, we compared leaf traits of species native to savanna and gallery (riverine) forests in the Cerrado region of central Brazil. 2. Congeneric species pairs from 14 different taxonomic families were studied, each with a savanna species and a forest species present at the study site. Only individuals growing in savanna conditions under full sun were studied. We measured foliar nutrients, delta13C, delta15N and specific leaf area (SLA: leaf area per unit leaf mass). We used phylogenetically independent contrasts to compare savanna and forest species and to test for correlations among species traits. 3. Overall, leaves of forest species had 17{\%} higher N concentration, 32{\%} higher P concentration, and 37{\%} higher K concentration, despite growing in similar soils. Concentrations of all three elements were strongly and positively correlated with SLA. 4. Forest species had 52{\%} greater SLA, on average, than savanna species, which accounts for the higher foliar nutrient concentrations of these species. 5. Savanna species had higher delta13C values than forest species, indicating higher water-use efficiency. The SLA was negatively correlated with delta13C, suggesting that SLA may also account for the higher water-use efficiency of savanna species. 6. There was no difference in foliar delta15N between savanna and forest species, but foliar delta15N was negatively correlated with soil pH. 7. These results contribute to recent studies showing that tropical savanna and forest species represent two distinct functional types, with large differences in ecology and physiology, that have important consequences for the dynamics of savanna-forest boundaries. Functional Ecology (2005) doi: 10.1111/j.1365-2435.2005.01045.x},
-author = {Hoffmann, W. A. and Franco, A. C. and Moreira, M. Z. and Haridasan, M.},
-doi = {10.1111/j.1365-2435.2005.01045.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Functional Ecology},
-number = {6},
-pages = {932--940},
-title = {{Specific leaf area explains differences in leaf traits between congeneric savanna and forest trees}},
-url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2435.2005.01045.x},
-volume = {19},
-year = {2005}
-}
-@phdthesis{Ayres1986,
-author = {Ayres, Jos{\'{e}} Marcio Corr{\^{e}}a},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ayres - 1986 - Uakaris and Amazonian flooded forest.pdf:pdf},
-number = {June},
-pages = {313},
-title = {{Uakaris and Amazonian flooded forest.}},
-year = {1986}
-}
-@book{Diggle2003,
-address = {London},
-author = {Diggle, Peter J.},
-edition = {2nd Editio},
-isbn = {978-0340740705},
-publisher = {Arnold},
-title = {{Statistical analysis of spatial point patterns}},
-year = {2003}
-}
-@article{Wagner2004,
-abstract = {Gradient analysis uses ordination methods to study the structure of biotic communities caused by biotic processes operating in a heterogeneous environment. This. structure has two spatial components: spatial processes within the community create autocorrelation, and the spatial structure of environmental factors creates spatial dependence. Ordination methods', however, do not make use of spatial information. Spatial alternatives are available in multivariate geostatistics, but are not compatible with important ordination methods used in gradient analysis, correspondence analysis and canonical correspondence analysis (CA, CCA). This paper shows how CA and CCA can be partitioned by distance (indirect and direct multi-scale ordination) and integrated with geostatistics. A diagnostic tool enables ecologists to partition ordination results by distance, to distinguish between components of spatial dependence and of spatial autocorrelation, and to check assumptions of independent residuals, stationarity, and scale-invariant correlation. The application is illustrated with a well-known data set of oribatid mites. Empirical chi-square variograms of individual species, their pair-wise cross variograms, and the variogram of the total inertia are defined and summarized in a variogram matrix, which leads to a spatial partitioning of the eigenvalues. The empirical variogram matrix provides a link to coregionalization analysis that may be used to simultaneously model spatial dependence and spatial autocorrelation. This will be useful for answering questions about the organism-specific scale of response to the environment, the optimal spacing of sampling units, or the scale-dependent effect of environmental factors.},
-author = {Wagner, Helene H.},
-doi = {10.1890/02-0738},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wagner - 2004 - Direct multi-scale ordination with canonical correspondence analysis.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {342--351},
-title = {{Direct multi-scale ordination with canonical correspondence analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/02-0738/abstract},
-volume = {85},
-year = {2004}
-}
-@article{Agapow2004,
-abstract = {Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48{\%}) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.},
-author = {Agapow, Paul Michael and Binindal-Emonds, Olaf R. P. and Crandall, Keith A. and Gittleman, John L. and Mace, Georgina M. and Marshall, Jonathon C. and Purvis, Andy},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Agapow et al. - 2004 - The impact of species concept on biodiversity studies.pdf:pdf},
-journal = {The Quarterly Review of Biology},
-number = {2},
-pages = {161--179},
-title = {{The impact of species concept on biodiversity studies}},
-url = {http://www.jstor.org/stable/10.1086/383542},
-volume = {79},
-year = {2004}
-}
-@book{Arbia1996,
-address = {Padova},
-author = {Arbia, Giuseppe and Espa, Giuseppe},
-publisher = {CEDAM},
-title = {{Statistica economica territoriale}},
-url = {https://www.libreriauniversitaria.it/statistica-economica-territoriale-arbia-giuseppe/libro/9788813199975},
-year = {1996}
-}
-@article{Hirsh1976,
-author = {Hirsh, S.},
-doi = {10.1093/oxfordjournals.oep.a041344},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hirsh - 1976 - An International Trade and Investment Theory of the Firm.pdf:pdf},
-journal = {Oxford Economic Papers},
-number = {2},
-pages = {258--270},
-title = {{An International Trade and Investment Theory of the Firm}},
-url = {http://academic.oup.com/oep/article/2360707/},
-volume = {28},
-year = {1976}
-}
-@article{Mulligan2005,
-abstract = {Analysts and policy makers frequently measure industrial localization and regional specialization. However, they rarely examine the nation's full array of industries or regions. So local indices, appropriate for specific industries or selected regions, are typically estimated. But in some instances global indices would be preferable in order to assess the wider features of the entire space-economy. This article constructs global indices from the local indices already used in assessing localization and specialization. Global localization and global specialization are shown to be identical when all local indices use the dissimilarity logic. Two-digit standard industry codes manufacturing data, taken from the U.S. during 1958-1995, are used to illustrate the results. The values of these global coefficients, like their local constituents, are shown to vary with geographic scale. The discussion addresses spatial distributions (evenness) but not geographic arrangements (clustering).},
-author = {Mulligan, G. F. and Schmidt, C.},
-doi = {10.1111/j.1468-2257.2005.00295.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mulligan, Schmidt - 2005 - A note on localization and specialization.pdf:pdf},
-journal = {Growth and Change},
-number = {4},
-pages = {565--576},
-title = {{A note on localization and specialization}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1468-2257.2005.00295.x/abstract},
-volume = {36},
-year = {2005}
-}
-@article{Simkin2011,
-abstract = {Scientists often re-invent things that were long known. Here we review these activities as related to the mechanism of producing power law distributions, originally proposed in 1922 by Yule to explain experimental data on the sizes of biological genera, collected by Willis. We also review the history of re-invention of closely related branching processes, random graphs and coagulation models.},
-annote = {doi: 10.1016/j.physrep.2010.12.004},
-author = {Simkin, M. V. and Roychowdhury, V. P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Simkin, Roychowdhury - 2011 - Re-inventing Willis.pdf:pdf},
-isbn = {0370-1573},
-journal = {Physics Reports},
-number = {1},
-pages = {1--35},
-title = {{Re-inventing Willis}},
-url = {http://www.sciencedirect.com/science/article/pii/S0370157310003339},
-volume = {502},
-year = {2011}
-}
-@article{Roggy2005,
-abstract = {This study looked at the interactive effects of tree architectural stage of development (ASD) and light availability on different plant traits (growth parameters, leaf morpho-anatomy and photosynthetic capacities) in the tropical species Dicorynia guianensis. A qualitative architectural analysis was used to categorize tree individuals sampled along a natural light gradient. The results show that some traits could have an ASD-dependence at the whole plant and leaf level without control of light. The changes observed relate to vigour thresholds the plant has to reach to shift from one ASD to another (i.e., the number of nodes and the internodes length per Growth Unit). Light conditions do not modify these thresholds but may modify the time they are crossed. Tree height was found strongly modulated by light conditions; hence, at a similar height, individuals may belong to different ASD. At the functional level, a decrease in Nm, and Amaxm was observed with increasing light availability, while Na increased and Amaxa remained unaffected. An ASD effect was also observed on Amaxa and LMA but not on Amaxm. These results demonstrated a weak ability of photosynthetic plasticity in response to light conditions, and that variations of leaf photosynthetic variables according to ASD can be explained by modifications in leaf nitrogen and LMA. Questions on the reliability of a height-based sampling strategy for evaluating the phenotypic plasticity of trees in relation to light conditions are raised.},
-author = {Roggy, Jean-Christophe and Nicolini, Eric and Imbert, Pascal and Caraglio, Yves and Bosc, Alexandre and Heuret, Patrick},
-doi = {10.1051/forest:2005048},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roggy et al. - 2005 - Links between tree structure and functional leaf traits in the tropical forest tree Dicorynia guianensis Amshoff (.pdf:pdf},
-journal = {Annals of Forest Science},
-pages = {553--564},
-title = {{Links between tree structure and functional leaf traits in the tropical forest tree Dicorynia guianensis Amshoff (Caesalpiniaceae)}},
-volume = {62},
-year = {2005}
-}
-@article{Jackson1993,
-abstract = {Approaches to determining the number of components to interpret from$\backslash$nprincipal components analysis were compared. Heuristic procedures$\backslash$nincluded: retaining components with eigenvalues (@ls) {\textgreater} 1 (i.e.,$\backslash$nKaiser-Guttman criterion); components with bootstrapped @ls {\textgreater} 1 (bootstrapped$\backslash$nKaiser-Guttman); the scree plot; the broken-stick model; and components$\backslash$nwith @ls totalling to a fixed amount of the total variance. Statistical$\backslash$napproaches included: Bartlett's test of sphericity; Bartlett's test$\backslash$nof homogeneity of the correlation matrix, Lawley's test of the second$\backslash$n@l; bootstrapped confidence limits on successive @l (i.e., significant$\backslash$ndifferences between @ls); and bootstrapped confidence limits on eigenvector$\backslash$ncoefficients (i.e., coefficients that differ significantly from zero).$\backslash$nAll methods were compared using simulated data matrices of uniform$\backslash$ncorrelation structure, patterned matrices of varying correlation$\backslash$nstructure and data sets of lake morphometry, water chemistry, and$\backslash$nbenthic invertebrate abundance. The most consistent results were$\backslash$nobtained from the broken-stick model and a combined measure using$\backslash$nbootstrapped @ls and associated eigenvector coefficients. The traditional$\backslash$nand bootstrapped Kaiser-Guttman approaches over-estimated the number$\backslash$nof nontrivial dimensions as did the fixed-amount-of-variance model.$\backslash$nThe scree plot consistently estimated one dimension more than the$\backslash$nnumber of simulated dimensions. Barlett's test of sphericity showed$\backslash$ninconsistent results. Both Bartlett's test of homogeneity of the$\backslash$ncorrelation matrix and Lawley's test are limited to testing for only$\backslash$none and two dimensions, respectively.},
-author = {Jackson, D. A.},
-doi = {10.2307/1939574},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jackson - 1993 - Stopping rules in principal components analysis A comparison of heuristical and statistical approaches(2).pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2204--2214},
-title = {{Stopping rules in principal components analysis: A comparison of heuristical and statistical approaches}},
-volume = {74},
-year = {1993}
-}
-@article{Porter1960,
-author = {Porter, Philip W.},
-doi = {10.1111/j.1467-8306.1960.tb00352.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Porter - 1960 - Earnest and the Orephagians A Fable of the Instruction of Young Geographers.pdf:pdf},
-journal = {Annals of the Association of American Geographers},
-number = {3},
-pages = {297--299},
-title = {{Earnest and the Orephagians: A Fable of the Instruction of Young Geographers}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8306.1960.tb00352.x/abstract},
-volume = {50},
-year = {1960}
-}
-@article{Black1999,
-author = {Black, Duncan and Henderson, J. Vernon},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Black, Henderson - 1999 - Spatial Evolution of Population and Industry in the United States.pdf:pdf},
-journal = {The American Economic Review},
-number = {2},
-pages = {321--327},
-title = {{Spatial Evolution of Population and Industry in the United States}},
-url = {http://www.jstor.org/stable/117129},
-volume = {89},
-year = {1999}
-}
-@article{Chase2011a,
-abstract = {Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition ($\beta$-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors.},
-author = {Chase, Jonathan M. and Myers, Jonathan A.},
-doi = {10.1098/rstb.2011.0063},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chase, Myers - 2011 - Disentangling the importance of ecological niches from stochastic processes across scales.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1576},
-pages = {2351--2363},
-title = {{Disentangling the importance of ecological niches from stochastic processes across scales}},
-url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2011.0063},
-volume = {366},
-year = {2011}
-}
-@article{OHara2005,
-abstract = {1. Several species richness estimators (two non-parametric, four based on rarefaction curves and two from fitting of abundance distributions) were compared by examining their performance in estimating the species richness for two moth data sets from the United Kingdom. Comparisons were also made using data simulated from the fitted abundance distributions. 2. The different species richness estimators gave different estimates. The non-parametric estimates and the rarefaction estimates were similar, but were smaller than the parametric estimates. When the simulated data were used, the only methods to give estimates near the true value was the parametric method using the distribution from which the data were simulated. 3. At present it is impossible to decide whether any of the estimation methods will give a realistic estimate, as not enough is known about the true numbers of species in communities. Until this is rectified, the most that can be hoped for is to obtain upper and lower bounds on species richness.},
-author = {O'Hara, R. B.},
-doi = {10.1111/j.1365-2656.2005.00940.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/O'Hara - 2005 - Species richness estimators How many species can dance on the head of a pin.pdf:pdf},
-journal = {Journal of Animal Ecology},
-pages = {375--386},
-title = {{Species richness estimators: How many species can dance on the head of a pin?}},
-volume = {74},
-year = {2005}
-}
-@misc{MENESR2008a,
-author = {MENESR},
-title = {{Le cahier de laboratoire national, pourquoi l'utiliser ?}},
-url = {https://intranet.inra.fr/mission{\_}qualite/content/download/2935/29766/version/1/file/CdL{\_}Pourquoi{\_}150206.pdf},
-year = {2008}
-}
-@article{Mora2011,
-abstract = {Knowing the number of species on Earth is one of the most basic yet elusive questions in science. Unfortunately, obtaining an accurate number is constrained by the fact that most species remain to be described and because indirect attempts to answer this question have been highly controversial. Here, we document that the taxonomic classification of species into higher taxonomic groups (from genera to phyla) follows a consistent pattern from which the total number of species in any taxonomic group can be predicted. Assessment of this pattern for all kingdoms of life on Earth predicts {\^{a}}ˆ¼8.7 million ({\^{A}}±1.3 million SE) species globally, of which {\^{a}}ˆ¼2.2 million ({\^{A}}±0.18 million SE) are marine. Our results suggest that some 86{\%} of the species on Earth, and 91{\%} in the ocean, still await description. Closing this knowledge gap will require a renewed interest in exploration and taxonomy, and a continuing effort to catalogue existing biodiversity data in publicly available databases.},
-author = {Mora, Camilo and Tittensor, Derek P. and Adl, Sina and Simpson, Alastair G. B. and Worm, Boris},
-doi = {10.1371/journal.pbio.1001127},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mora et al. - 2011 - How Many Species Are There on Earth and in the Ocean.pdf:pdf},
-journal = {PLoS Biology},
-number = {8},
-pages = {e1001127},
-title = {{How Many Species Are There on Earth and in the Ocean?}},
-url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001127},
-volume = {9},
-year = {2011}
-}
-@article{Loreau2001a,
-abstract = {The impact of biodiversity loss on the functioning of ecosystems and their ability to provide ecological services has become a central issue in ecology. Several experiments have provided evidence that reduced species diversity may impair ecosystem processes such as plant biomass production. The interpretation of these experiments, however, has been controversial because two types of mechanism may operate in combination. In the 'selection effect', dominance by species with particular traits affects ecosystem processes. In the 'complementarity effect', resource partitioning or positive interactions lead to increased total resource use. Here we present a new approach to separate the two effects on the basis of an additive partitioning analogous to the Price equation in evolutionary genetics. Applying this method to data from the pan-European BIODEPTH experiment reveals that the selection effect is zero on average and varies from negative to positive in different localities, depending on whether species with lower- or higher-than-average biomass dominate communities. In contrast, the complementarity effect is positive overall, supporting the hypothesis that plant diversity influences primary production in European grasslands through niche differentiation or facilitation.},
-author = {Loreau, Michel and Hector, Andrew},
-doi = {10.1038/35083573},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau, Hector - 2001 - Partitioning selection and complementarity in biodiversity experiments.pdf:pdf},
-journal = {Nature},
-pages = {72--76},
-title = {{Partitioning selection and complementarity in biodiversity experiments}},
-url = {http://www.nature.com/nature/journal/v412/n6842/full/412072a0.html},
-volume = {412},
-year = {2001}
-}
-@article{Co2002,
-abstract = {Agglomeration in U.S. manufacturing is more common than initially thought. This clustering arises from location natural advantages and spillovers. Extant studies on agglomeration do not distinguish the activities of U.S.-owned plants from those that are foreign owned. This distinction is crucial since policies seem to have differential impacts on both types of plants. I find that industry scale, resource intensity and urbanization economies have larger impacts on foreign plant agglomeration whereas knowledge intensity has a larger effect on domestic plant agglomeration.},
-author = {Co, Catherine Y.},
-doi = {10.1007/s001680200099},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Co - 2002 - The agglomeration of U.S.-owned and foreign-owned plants across the U.S. States.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {4},
-pages = {575--592},
-title = {{The agglomeration of U.S.-owned and foreign-owned plants across the U.S. States}},
-url = {https://link.springer.com/article/10.1007/s001680200099},
-volume = {36},
-year = {2002}
-}
-@article{Arbia2014,
-abstract = {The study of the geographical distribution of firms and of the dynamic pattern of firm entry and firm exits is a particularly relevant issue in regional health economics especially in the view of policy intervention to geographically balance health service supply and demand. The current state of the art in the study of new firm formation and firm exit (see, e.g., Armington and Acs, 2002; Folta et al., 2006; Andersson and Koster, 2011; Raspe and van Oort, 2011) collects a comprehensive set of empirical methodologies for data aggregated at the macro (national) or meso (e.g. regional) territorial levels, in which observations typically consist of the administrative units (such as regions, counties and municipalities). The lack of a systematic approach to the analysis of data at the micro-territorial level - where the observations refer to the geographical coordinates of each individual firm - has dramatically limited the possibility to obtain robust evidences about firm demography phenomenon mainly due to a problem of data scarcity and reliability. To overcome such limitations, in this article we propose an approach to the analysis of the spatial dynamics of firm formation/exit based on micro-geographic data. In particular, we illustrate the use the space- time inhomogeneous K-function (Gabriel and Diggle, 2009) to detect the spatio-temporal clustering of firm entries and firm exits generated by the interaction between economic agents while controlling for common (locally varying) factors, spatial and temporal heterogeneity. In view of our aim the present paper shosw the results of an empirical application of the methodology to the case of new firms entry and firm exit in the pharmaceutical and medical device manufacturing industry during the years 2004-2009 in an Italian region (Veneto).},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego and Dickson, Maria Michela},
-doi = {10.1016/j.regsciurbeco.2014.10.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2014 - Spatio-temporal clustering in the pharmaceutical and medical device manufacturing industry A geographical micro-le.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-pages = {298--304},
-title = {{Spatio-temporal clustering in the pharmaceutical and medical device manufacturing industry: A geographical micro-level analysis}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0166046214001045},
-volume = {49},
-year = {2014}
-}
-@phdthesis{Combes1995,
-address = {Paris},
-author = {Combes, Pierre-Philippe},
-publisher = {Ecole des Hautes Etudes en Sciences Sociales},
-title = {{Int{\'{e}}gration {\'{e}}conomique : Localisation et R{\'{e}}gulation des Entreprises}},
-year = {1995}
-}
-@article{Suominen2013,
-abstract = {Soil quality is an important determinant of primary productivity and species occurrence patterns. Therefore, plant species composition can be used as an indicator of soil quality when direct sampling of soils is impractical. * We test how well the species composition of the plant family Melastomataceae can predict soil properties in western Amazonian rain forests. We examine nine soil variables: pH; loss-on-ignition; the concentrations of Al and P; and the concentrations of Ca, K, Mg, Na and the sum of these base cations. We compare two commonly used prediction techniques, k-nearest neighbour (k-NN) estimation and weighted averaging calibration via species indicator values. The Melastomataceae and soil data come from 311 localities widely distributed in western Amazonia. We use two different sets of Melastomataceae: a full set including all 283 observed species and an easy set containing 58 species that are both abundant in the data set and relatively easy to identify in the field. * Weighted averaging calibration and k-NN performed approximately equally well. Both were found to be useful techniques to convert information on Melastomataceae species composition to estimates of soil cation concentration, especially magnesium and calcium, and to a lesser degree potassium. In nearly all cases, the full set of Melastomataceae species gave more accurate predictions than the easy set, but the differences were relatively small. * Synthesis and applications. Our results show that Melastomataceae can be used as an indicator group that facilitates the field estimation of soil cation concentration and hence the assessment and mapping of soil variation over large areas. This provides important background information for all types of land-use planning, including systematic conservation planning that aims at representativeness of conservation area networks.},
-author = {Suominen, Lassi and Ruokolainen, Kalle and Tuomisto, Hanna and Llerena, Nelly and Higgins, Mark A},
-doi = {10.1111/1365-2664.12131},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Suominen et al. - 2013 - Predicting soil properties from floristic composition in western Amazonian rain forests performance of k-neares.pdf:pdf},
-journal = {Journal of Applied Ecology},
-number = {6},
-pages = {1441--1449},
-title = {{Predicting soil properties from floristic composition in western Amazonian rain forests: performance of k-nearest neighbour estimation and weighted averaging calibration}},
-url = {http://dx.doi.org/10.1111/1365-2664.12131},
-volume = {50},
-year = {2013}
-}
-@article{Kraft2011,
-abstract = {Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites (beta diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in beta diversity caused simply by changes in the sizes of species pools. For example, forest inventories sampled along latitudinal and elevational gradients show the well-documented pattern that beta diversity is higher in the tropics and at low elevations. However, after correcting for variation in pooled species richness (gamma diversity), these differences in beta diversity disappear. Therefore, there is no need to invoke differences in the mechanisms of community assembly in temperate versus tropical systems to explain these global-scale patterns of beta diversity.},
-annote = {ISI Document Delivery No.: 823KQ
-Times Cited: 13
-Cited Reference Count: 34
-Kraft, Nathan J. B. Comita, Liza S. Chase, Jonathan M. Sanders, Nathan J. Swenson, Nathan G. Crist, Thomas O. Stegen, James C. Vellend, Mark Boyle, Brad Anderson, Marti J. Cornell, Howard V. Davies, Kendi F. Freestone, Amy L. Inouye, Brian D. Harrison, Susan P. Myers, Jonathan A.
-National Center for Ecological Analysis and Synthesis (NCEAS); NSF[EF-0553768, DBI-0906005]; University of California, Santa Barbara; state of California; National Science and Engineering Research Council of Canada; U.S. Department of Energy[DE-FG02-08ER64510]
-We are grateful to A. H. Gentry, the Missouri Botanical Garden, and numerous additional collectors who contributed to the latitudinal data set. The data sets are available in the original publications or electronically from SALVIAS (www.salvias.net). This work was conducted as part of the Gradients of beta-diversity Working Group supported by the National Center for Ecological Analysis and Synthesis (NCEAS), a center funded by NSF (grant EF-0553768); the University of California, Santa Barbara; and the state of California. N.J.B.K. was supported by the National Science and Engineering Research Council of Canada CREATE Training Program in Biodiversity Research. L. S. C. was supported by an NCEAS postdoctoral fellowship. N.J.S. was supported by U.S. Department of Energy Program for Ecosystem Research DE-FG02-08ER64510. J.C.S. was supported by an NSF Postdoctoral Fellowship in Bioinformatics (DBI-0906005).
-Amer assoc advancement science
-Washington},
-author = {Kraft, Nathan J. B. and Comita, Liza S. and Chase, Jonathan M. and Sanders, Nathan J. and Swenson, Nathan G. and Crist, Thomas O. and Stegen, James C. and Vellend, Mark and Boyle, Brad and Anderson, Marti J. and Cornell, Howard V. and Davies, Kendi F. and Freestone, Amy L. and Inouye, Brian D. and Harrison, Susan P. and Myers, Jonathan A.},
-doi = {10.1126/science.1208584},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kraft et al. - 2011 - Disentangling the Drivers of beta Diversity Along Latitudinal and Elevational Gradients.pdf:pdf},
-journal = {Science},
-number = {6050},
-pages = {1755--1758},
-title = {{Disentangling the Drivers of beta Diversity Along Latitudinal and Elevational Gradients}},
-url = {http://science.sciencemag.org/content/333/6050/1755},
-volume = {333},
-year = {2011}
-}
-@book{Mabberley1983,
-abstract = {A textbook in the Tertiary Level Biology series, designed for advanced undergraduates. There are 9 chapters: The tropical rain forest; The changing physical setting - continental drift and tropical climate; Soils and nutrients; The changing biological framework - succession; The components of diversity; Species richness; Coevolution and coexistence - pollination, seed dispersal and predation, herbivory; Rain-forest man; and The changing forest today. An index is included.},
-author = {Mabberley, D J},
-booktitle = {Tropical rain forest ecology.},
-isbn = {0-216-91510-4$\backslash$0-216-91509-0$\backslash$0-412-00441-0},
-title = {{Tropical rain forest ecology}},
-year = {1983}
-}
-@article{Marion2015,
-abstract = {Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity ($\alpha$ diversity) and between-individual components ($\beta$ diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.},
-author = {Marion, Zachary H. and Fordyce, James A. and Fitzpatrick, Benjamin M.},
-doi = {10.1086/682369},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marion, Fordyce, Fitzpatrick - 2015 - Extending the concept of diversity partitioning to characterize phenotypic complexity.pdf:pdf},
-journal = {The American naturalist},
-number = {3},
-pages = {348--361},
-title = {{Extending the concept of diversity partitioning to characterize phenotypic complexity}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/682369?journalCode=an},
-volume = {186},
-year = {2015}
-}
-@article{Chao2009,
-abstract = {Biodiversity sampling is labor intensive, and a substantial fraction of a biota is often represented by species of very low abundance, which typically remain undetected by biodiversity surveys. Statistical methods are widely used to estimate the asymptotic number of species present, including species not yet detected. Additional sampling is required to detect and identify these species, but richness estimators do not indicate how much sampling effort (additional individuals or samples) would be necessary to reach the asymptote of the species accumulation curve. Here we develop the first statistically rigorous nonparametric method for estimating the minimum number of additional individuals, samples, or sampling area required to detect any arbitrary proportion (including 100{\%}) of the estimated asymptotic species richness. The method uses the Chao1 and Chao2 nonparametric estimators of asymptotic richness, which are based on the frequencies of rare species in the original sampling data. To evaluate the performance of the proposed method, we randomly subsampled individuals or quadrats from two large biodiversity inventories (light trap captures of Lepidoptera in Great Britain and censuses of woody plants on Barro Colorado Island [BCI], Panama). The simulation results suggest that the method performs well but is slightly conservative for small sample sizes. Analyses of the BCI results suggest that the method is robust to nonindependence arising from small-scale spatial aggregation of species occurrences. When the method was applied to seven published biodiversity data sets, the additional sampling effort necessary to capture all the estimated species ranged from 1.05 to 10.67 times the original sample (median'2.23). Substantially less effort is needed to detect 90{\%}of the species (0.33–1.10 times the original effort; median ' 0.80). An Excel spreadsheet tool is provided for calculating necessary sampling effort for either abundance data or replicated incidence data.},
-author = {Chao, Anne and Colwell, Robert K. and Lin, Chih-Wei and Gotelli, Nicholas J.},
-doi = {10.1890/07-2147.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2009 - Sufficient sampling for asymptotic minimum species richness estimators.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1125--1133},
-title = {{Sufficient sampling for asymptotic minimum species richness estimators}},
-url = {http://dx.doi.org/10.1890/07-2147.1},
-volume = {90},
-year = {2009}
-}
-@article{Sheldon1969,
-abstract = {Three measures of equitability or relative diversity are shown to be dependent on the species count component of total diversity. This dependence limits the use of equitability indices as comparative statistics.},
-author = {Sheldon, Andrew L.},
-doi = {10.2307/1933900},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sheldon - 1969 - Equitability indices dependence on the species count.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {466--467},
-title = {{Equitability indices: dependence on the species count}},
-url = {http://www.fcnym.unlp.edu.ar/catedras/ecocomunidades/Sheldon - Equitability Indices-- Dependence on the Species Count.pdf},
-volume = {50},
-year = {1969}
-}
-@article{Wright2002b,
-abstract = {Evidence concerning mechanisms hypothesized to explain species coexistence in hyper-diverse communities is reviewed for tropical forest plants. Three hypotheses receive strong support. Niche differences are evident from non-random spatial distributions along micro-topographic gradients and from a survivorshipgrowth tradeoff during regeneration. Host-specific pests reduce recruitment near reproductive adults (the Janzen-Connell effect), and, negative density dependence occurs over larger spatial scales among the more abundant species and may regulate their populations. A fourth hypothesis, that suppressed understory plants rarely come into competition with one another, has not been considered before and has profound implications for species coexistence. These hypotheses are mutually compatible. Infrequent competition among suppressed understory plants, niche differences, and Janzen-Connell effects may facilitate the coexistence of the many rare plant species found in tropical forests while negative density dependence regulates the few most successful and abundant species.},
-author = {Wright, Joseph S. and Wright, S. Joseph},
-doi = {10.1007/s004420100809},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright - 2002 - Plant diversity in tropical forests a review of mechanisms of species coexistence.pdf:pdf},
-journal = {Oecologia},
-number = {1},
-pages = {1--14},
-title = {{Plant diversity in tropical forests: a review of mechanisms of species coexistence}},
-url = {http://link.springer.com/10.1007/s004420100809},
-volume = {130},
-year = {2002}
-}
-@article{Takada2015,
-abstract = {In order to develop a composite measure of community species diversity and abundance, a generalization of Morisita's prosperity index is proposed. Using Hill's diversity representation, the prosperity index is a product of the total number of individuals and the effective number of species in a community. A series of prosperity indices can be derived using a parameter (Hill's number). As an analogy of component partitions of species diversity, regional, within, and between components are also defined. The prosperity index will be useful for practical aspects related to conservation and management.},
-author = {Takada, Yoshitake},
-doi = {10.1007/s10531-015-0933-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Takada - 2015 - Morisita's prosperity index revisited.pdf:pdf},
-journal = {Biodiversity and Conservation},
-number = {8},
-pages = {2093--2097},
-title = {{Morisita's prosperity index revisited}},
-url = {http://link.springer.com/10.1007/s10531-015-0933-5},
-volume = {24},
-year = {2015}
-}
-@article{Spehn2002,
-abstract = {To investigate how plant diversity loss affects nitrogen accumulation in above-ground plant biomass and how consistent patterns are across sites of different climatic and soil conditions, we varied the number of plant species and functional groups (grasses, herbs and legumes) in experimental grassland communities across seven European experimental sites (Switzerland, Germany, Ireland, United Kingdom (Silwood Park), Portugal, Sweden and Greece). Nitrogen pools were significantly affected by both plant diversity and community composition. Two years after sowing, nitrogen pools in Germany and Switzerland strongly increased in the presence of legumes. Legume effects on nitrogen pools were less pronounced at the Swedish, Irish and Portuguese site. In Greece and UK there were no legume effects. Nitrogen concentration in total above-ground biomass was quite invariable at 1.66 +/- 0.03{\%} across all sites and diversity treatments. Thus, the presence of legumes had a positive effect oil nitrogen pools by significantly increasing above-ground biomass, i.e. by increases in vegetation quantity rather than quality. At the German site with the strongest legume effect on nitrogen pools and biomass, nitrogen that was fixed symbiotically by legumes was transferred to the other plant functional groups (grasses and herbs) but varied depending on the particular legume species fixing N and the non-legume species taking it up. Nitrogenfixation by legumes therefore appeared to be one of the major functional traits of species that influenced nitrogen accumulation and biomass production, although effects varied among sites and legume species. This study demonstrates that the consequences of species loss on the nitrogen budget of plant communities may be more severe if legume species are lost. However, our data indicate that legume species differ in their N-2 fixation. Therefore, loss of an efficient N-2-fixer (Trifolium in our study) may have a greater influence on the ecosystem function than loss of a less efficient species (Lotus in our study). Furthermore, there is indication that P availability in the soil facilitates the legume effect on biomass production and biomass nitrogen accumulation.},
-author = {Spehn, E. M. and Scherer-Lorenzen, M. and Schmid, B. and Hector, Andrew and Caldeira, M. C. and Dimitrakopoulos, P. G. and Finn, J. A. and Jumpponen, A. and O'Donnovan, G. and Pereira, J. S. and Schulze, Ernst-Detlef and Troumbis, A. Y. and K{\"{o}}rner, C.},
-doi = {10.1034/j.1600-0706.2002.980203.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Spehn et al. - 2002 - The role of legumes as a component of biodiversity in a cross-European study of grassland biomass nitrogen.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {205--218},
-title = {{The role of legumes as a component of biodiversity in a cross-European study of grassland biomass nitrogen}},
-url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2002.980203.x/full},
-volume = {98},
-year = {2002}
-}
-@article{Hou2014,
-abstract = {In density estimation task, Maximum Entropy (Maxent) model can effectively use reliable prior information via nonparametric constraints, that is, linear constraints without empirical parameters. However, reliable prior information is often insufficient, and parametric constraints becomes necessary but poses considerable implementation complexity. Improper setting of parametric constraints can result in overfitting or underfitting. To alleviate this problem, a generalization of Maxent, under Tsallis entropy framework, is proposed. The proposed method introduces a convex quadratic constraint for the correction of (expected) quadratic Tsallis Entropy Bias (TEB). Specifically, we demonstrate that the expected quadratic Tsallis entropy of sampling distributions is smaller than that of the underlying real distribution with regard to frequentist, Bayesian prior, and Bayesian posterior framework, respectively. This expected entropy reduction is exactly the (expected) TEB, which can be expressed by the closed-form formula and acts as a consistent and unbiased correction with an appropriate convergence rate. TEB indicates that the entropy of a specific sampling distribution should be increased accordingly. This entails a quantitative reinterpretation of the Maxent principle. By compensating TEB and meanwhile forcing the resulting distribution to be close to the sampling distribution, our generalized quadratic Tsallis Entropy Bias Compensation (TEBC) Maxent can be expected to alleviate the overfitting and underfitting. We also present a connection between TEB and Lidstone estimator. As a result, TEB–Lidstone estimator is developed by analytically identifying the rate of probability correction in Lidstone. Extensive empirical evaluation shows promising performance of both TEBC Maxent and TEB-Lidstone in comparison with various state-of-the-art density estimation methods.},
-author = {Hou, Yuexian and Wang, Bo and Song, Dawei and Cao, Xiaochun and Li, Wenjie},
-doi = {10.1111/j.1467-8640.2012.00443.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hou et al. - 2014 - Quadratic Tsallis Entropy Bias and Generalized Maximum Entropy Models.pdf:pdf},
-journal = {Computational Intelligence},
-number = {2},
-pages = {233--262},
-title = {{Quadratic Tsallis Entropy Bias and Generalized Maximum Entropy Models}},
-url = {http://doi.wiley.com/10.1111/j.1467-8640.2012.00443.x},
-volume = {30},
-year = {2014}
-}
-@article{Pavoine2013a,
-abstract = {To evaluate rates of evolution, to establish tests of correlation between two traits, or to investigate to what degree the phylogeny of a species assemblage is predictive of a trait value so-called tests for phylogenetic signal are used. Being based on different approaches, these tests are generally thought to possess quite different statistical performances. In this article, we show that the Blomberg et al. K and K*, the Abouheif index, the Moran's I, and the Mantel correlation are all based on a cross-product statistic, and are thus all related to each other when they are associated to a permutation test of phylogenetic signal. What changes is only the way phylogenetic and trait similarities (or dissimilarities) among the tips of a phylogeny are computed. The definitions of the phylogenetic and trait-based (dis)similarities among tips thus determines the performance of the tests. We shortly discuss the biological and statistical consequences (in terms of power and type I error of the tests) of the observed relatedness among the statistics that allow tests for phylogenetic signal. Blomberg et al. K* statistic appears as one on the most efficient approaches to test for phylogenetic signal. When branch lengths are not available or not accurate, Abouheif's Cmean statistic is a powerful alternative to K*. {\textcopyright} 2012 The Author(s). Evolution {\textcopyright} 2012 The Society for the Study of Evolution.},
-annote = {Cited By (since 1996):2
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: EVOLA
-PubMed ID: 23461331
-Language of Original Document: English
-Correspondence Address: Pavoine, S.; Mus{\'{e}}um national d'Histoire naturelle, D{\'{e}}partement Ecologie et Gestion de la Biodiversit{\'{e}}, UMR 7204 CNRS UPMC, 55-61 rue Buffon, 75005 Paris, France; email: pavoine@mnhn.fr},
-author = {Pavoine, Sandrine and Ricotta, Carlo},
-doi = {10.1111/j.1558-5646.2012.01823.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Ricotta - 2013 - Testing for phylogenetic signal in biological traits The ubiquity of cross-product statistics.pdf:pdf},
-journal = {Evolution},
-number = {3},
-pages = {828--840},
-title = {{Testing for phylogenetic signal in biological traits: The ubiquity of cross-product statistics}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84874721929{\&}partnerID=40{\&}md5=c32260cf1646861a389a49e850330022},
-volume = {67},
-year = {2013}
-}
-@article{Gatrell1996,
-abstract = {This paper reviews a number of methods for the exploration and modelling of spatial point patterns with particular reference to geographical epidemiology (the geographical incidence of disease). Such methods go well beyond the conventional 'nearest-neighbour' and 'quadrat' analyses which have little to offer in an epidemiological context because they fail to allow for spatial variation in population density. Correction for this is essential if the aim is to assess the evidence for 'clustering' of cases of disease. We examine methods for exploring spatial variation in disease risk, spatial and space-time clustering, and we consider methods for modelling the raised incidence of disease around suspected point sources of pollution. All methods are illustrated by reference to recent case studies including child cancer incidence, Burkitt's lymphoma, cancer of the larynx and childhood asthma. An Appendix considers a range of possible software environments within which to apply these methods. The links to modern geographical information systems are discussed. key},
-author = {Gatrell, Antony C. and Bailey, Trevor C. and Diggle, Peter J. and Rowlingson, Barry S.},
-doi = {10.2307/622936},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gatrell et al. - 1996 - Spatial point pattern analysis and its application in geographical epidemiology.pdf:pdf},
-journal = {Transactions of the Institute of British Geographers},
-number = {1},
-pages = {256--274},
-title = {{Spatial point pattern analysis and its application in geographical epidemiology}},
-url = {http://www.jstor.org/stable/622936},
-volume = {21},
-year = {1996}
-}
-@article{Tsai2015,
-author = {Tsai, Cheng-Han and Lin, Yi-Ching and Wiegand, Thorsten and Nakazawa, Takefumi and Su, Sheng-Hsin and Hsieh, Chih-Hao and Ding, Tzung-Su},
-doi = {10.1371/journal.pone.0124539},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsai et al. - 2015 - Individual Species-Area Relationship of Woody Plant Communities in a Heterogeneous Subtropical Monsoon Rainforest.pdf:pdf},
-issn = {1932-6203},
-journal = {Plos One},
-number = {4},
-pages = {e0124539},
-title = {{Individual Species-Area Relationship of Woody Plant Communities in a Heterogeneous Subtropical Monsoon Rainforest}},
-url = {http://dx.plos.org/10.1371/journal.pone.0124539},
-volume = {10},
-year = {2015}
-}
-@article{Faith1992,
-abstract = {Protecting biological diversity with limited resources may require placing conservation priorities on different taxa. A system of priorities that reflects the value of taxonomic diversity can be achieved by setting priorities such that the subset of taxa that is protected has maximum underlying feature diversity. Such feature diversity of taxon subsets is difficult to estimate directly, but can be predicted by the cladistic/phylogenetic relationships among the taxa. In this study, a simple measure of phylogenetic diversity is defined based on cladistic information. The measure of phylogenetic diversity, PD, is contrasted with a measure of taxic diversity recently developed by Vane-Wright et al. (Biol. Conserv., 55, 1991). In re-examining reserve-selection scenarios based on a phylogeny of bumble bees (Apidae), PD produces quite different priorities for species conservation, relative to taxic diversity. The potential application of PD at levels below that of the species is then illustrated using a mtDNA phylogeny for populations of crested newts Triturus cristatus. Calculation of PD for different population subsets shows that protection of populations at either of two extremes of the geographic range of the group can significantly increase the phylogenetic diversity that is protected. {\^{A}}{\textcopyright} 1992.},
-annote = {Cited By (since 1996): 408
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: BICOB
-Language of Original Document: English
-Correspondence Address: Faith, D.P.; Division of Wildlife and Ecology, CSIRO, PO Box 84, Lyneham, ACT 2602, Australia},
-author = {Faith, Daniel P.},
-doi = {10.1016/0006-3207(92)91201-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faith - 1992 - Conservation evaluation and phylogenetic diversity.pdf:pdf},
-journal = {Biological Conservation},
-number = {1},
-pages = {1--10},
-title = {{Conservation evaluation and phylogenetic diversity}},
-url = {http://www.sciencedirect.com/science/article/pii/0006320792912013},
-volume = {61},
-year = {1992}
-}
-@phdthesis{Roggy1998,
-author = {Roggy, Jean-Christophe},
-publisher = {Universit{\'{e}} Claude Bernard, Lyon I},
-title = {{Contribution des symbioses fixatrices d'azote {\`{a}} la stabilit{\'{e}} de l'{\'{e}}cosyst{\`{e}}me forestier tropical guyanais}},
-year = {1998}
-}
-@article{Grabchak2015,
-abstract = {Turing's formula is an amazing result that allows one to estimate the probability of observing something that has not been observed before. After a brief review of the literature, we perform a simulation study to better understand how well this formula works in a variety of situations. We also compare the performance of Turing's formula with several modifications that have appeared in the literature. We find that these modifications tend to outperform Turing's formula, but usually not by very much. We further find that Turing's formula and its modifications tend to work better for heavy-tailed distributions than for light-tailed ones.},
-author = {Grabchak, Michael and Cosme, Victor},
-doi = {10.1080/03610918.2015.1109658},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grabchak, Cosme - 2015 - On The Performance of Turing's Formula A Simulation Study.pdf:pdf},
-journal = {Communications in Statistics - Simulation and Computation},
-title = {{On The Performance of Turing's Formula: A Simulation Study}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/03610918.2015.1109658?journalCode=lssp20},
-volume = {in press},
-year = {2015}
-}
-@article{Baddeley2000a,
-abstract = {The interaction between points in a spatial point process can be measured by its empty space function F, its nearest-neighbour distance distribution function G, and by combinations such as the J function J = (1 G)/(1 F). The estimation of these functions is hampered by edge effects: the uncorrected, empirical distributions of distances observed in a bounded sampling window W give severely biased estimates of F and G. However, in this paper we show that the corresponding uncorrected estimator of the function J = (1 G)/(1 F) is approximately unbiased for the Poisson case, and is useful as a summary statistic. Specifically, consider the estimate W of J computed from uncorrected estimates of F and G. The function JW(r), estimated by W, possesses similar properties to the J function, for example JW(r) is identically 1 for Poisson processes. This enables direct interpretation of uncorrected estimates of J, something not possible with uncorrected estimates of either F, G or K. We propose a Monte Carlo test for complete spatial randomness based on testing whether JW(r) 1. Computer simulations suggest this test is at least as powerful as tests based on edge corrected estimators of J.},
-author = {Baddeley, Adrian J. and Kerscher, M. and Schladitz, K. and Scott, B. T.},
-doi = {10.1111/1467-9574.00143},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley et al. - 2000 - Estimating the J function without edge correction.pdf:pdf},
-journal = {Statistica Neerlandica},
-number = {3},
-pages = {315--328},
-title = {{Estimating the J function without edge correction}},
-url = {http://www.blackwell-synergy.com/links/doi/10.1111/1467-9574.00143},
-volume = {54},
-year = {2000}
-}
-@article{Faller2008,
-abstract = {Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the unknown subset of current species that will still be present at some future time, then this 'future phylogenetic diversity' provides a measure of the impact of various extinction scenarios in biodiversity conservation. In this paper, we study the distribution of future phylogenetic diversity under a simple model of extinction (a generalized 'field of bullets' model). We show that the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows, under mild conditions, which are necessary. We also describe an algorithm to compute the distribution efficiently, provided the edge lengths are integral, and briefly outline the significance of our findings for biodiversity conservation. ?? 2007 Elsevier Ltd. All rights reserved.},
-author = {Faller, Be{\'{a}}ta and Pardi, Fabio and Steel, Mike},
-doi = {10.1016/j.jtbi.2007.11.034},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faller, Pardi, Steel - 2008 - Distribution of phylogenetic diversity under random extinction.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {2},
-pages = {286--296},
-title = {{Distribution of phylogenetic diversity under random extinction}},
-volume = {251},
-year = {2008}
-}
-@article{Cornell2014,
-abstract = {A regional species pool comprises all species available to colonize a focal site. The roots of the concept are imbedded in island biogeography the-ory, supply-side ecology, and early propagule addition experiments. The pool concept allows ecologists to examine large-scale effects—including ge-ographic area, evolutionary age, and immigration and diversification—on the diversity, composition, and phylogenetic structure of local communi-ties. Both theory and evidence show that pool influences are greatest when local communities are not strongly and predictably structured by species interactions (e.g., under frequent disturbance or if many species are rare). Practical and conceptual issues to consider when delineating species pools include choosing an appropriate spatial scale, whether to account for envi-ronmental filtering, whether to include the species within a fixed geographic area versus those whose geographic ranges overlap with a site, or whether to use databases or geographic data sources. Each issue is discussed in the context of 63 studies using the species pool approach. We conclude that the species pool concept has contributed greatly to our understanding of com-munity dynamics by bridging the gap between large and small spatial scales. Future studies must compare pool characteristics with community structure across multiple regions for a more complete understanding of community assembly.},
-author = {Cornell, Howard V. and Harrison, Susan P.},
-doi = {10.1146/annurev-ecolsys-120213-091759},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cornell, Harrison - 2014 - What Are Species Pools and When Are They Important.pdf:pdf},
-journal = {Annual Review of Ecology, Evolution, and Systematics},
-number = {1},
-pages = {45--67},
-title = {{What Are Species Pools and When Are They Important?}},
-url = {http://www.annualreviews.org/doi/10.1146/annurev-ecolsys-120213-091759},
-volume = {45},
-year = {2014}
-}
-@article{Petchey2002,
-abstract = {Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity ‘‘FD'' is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.},
-author = {Petchey, Owen L. and Gaston, Kevin J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Petchey, Gaston - 2002 - Functional diversity (FD), species richness and community composition.pdf:pdf},
-journal = {Ecology Letters},
-pages = {402--411},
-title = {{Functional diversity (FD), species richness and community composition}},
-volume = {5},
-year = {2002}
-}
-@article{Kraft2002,
-abstract = {Assessing the spatial distribution of organisms across landscapes is a key step toward determining processes that produce observed patterns. The spatial distribution of an invasive aquatic mollusk, the zebra mussel (Dreissena polymorpha), was examined in two lake-rich areas (Belarus and midwestern United States) with contrasting invasion histories. Spatial distribution patterns of invaded lakes were determined using Ripley's K. Aggregation of invaded lakes was found at similar spatial extents ({\textless}50 km) in both regions; segregation was found at spatial extents {\textgreater}120 km in Belarus. The observed spatial extent of aggregation likely reflected the scale of secondary geographic spread, whereas the scale of long-distance dispersal events was reflected by the spatial extent of segregation. Isolated Belarus lakes were less likely to be invaded than those connected by waterways. Although one-dimensional aggregation of invaded lakes along connected Belarus waterways was not observed, nearest neighbor analysis indicated that zebra mussel dispersal occurred at distances {\textless}15 km within these waterways. Based on observed spatial pattern, we concluded that zebra mussels have not yet saturated European and North American lake landscapes, including many suitable lakes. Similar distribution patterns of invaded lakes in Belarus and North America suggest that similar processes have influenced zebra mussel spread in both landscapes.},
-annote = {Article
-English
-ECOL APPL
-553UL},
-author = {Kraft, Clifford E. and Sullivan, Patrick J. and Karatayev, Alexander Y. and Burlakova, Lyubov E. and Nekola, Jeffrey C. and Johnson, Ladd E. and Padilla, Dianna K.},
-doi = {10.2307/3060986},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kraft et al. - 2002 - Landscape patterns of an aquatic invader Assessing dispersal extent from spatial distributions.pdf:pdf},
-journal = {Ecological Applications},
-number = {3},
-pages = {749--759},
-title = {{Landscape patterns of an aquatic invader: Assessing dispersal extent from spatial distributions}},
-url = {https://www.jstor.org/stable/3060986},
-volume = {12},
-year = {2002}
-}
-@article{Curry1983,
-author = {Curry, B. and George, K. D.},
-doi = {10.2307/2097885},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Curry, George - 1983 - Industrial Concentration a Survey.pdf:pdf},
-journal = {The Journal of Industrial Economics},
-number = {3},
-pages = {203--255},
-title = {{Industrial Concentration: a Survey}},
-url = {https://www.jstor.org/stable/2097885},
-volume = {31},
-year = {1983}
-}
-@article{Hutchinson1957a,
-abstract = {Excerpt This concluding survey1 of the problems considered in the Symposium naturally falls into three sections. In the first brief section certain of the areas in which there is considerable difference in outlook are discussed with a view to ascertaining the nature of the differences in the points of view of workers in different parts of the field; no aspect of the Symposium has been more important than the reduction of areas of dispute. In the second section a rather detailed analysis of one particular problem is given, partly because the question, namely, the nature of the ecological niche and the validity of the principle of niche specificity has raised and continues to raise difficulties, and partly because discussion of this problem gives an opportunity to refer to new work of potential importance not otherwise considered in the Symposium. The third section deals with possible directions for future research. The Demographic},
-archivePrefix = {arXiv},
-arxivId = {1009.4607v1},
-author = {Hutchinson, G. Evelyn},
-doi = {10.4324/9781315674315},
-eprint = {1009.4607v1},
-isbn = {9781317378792},
-issn = {0939-1517},
-journal = {Population Studies: Animal Ecology and Demography. Cold Spring Harbor SYmposia on Quantitative Biology},
-pages = {415--427},
-pmid = {21537607},
-title = {{Concluding remarks on the cold Spring Harbor Symposia on Quantitative Biology}},
-volume = {22},
-year = {1957}
-}
-@article{Keitt2002,
-abstract = {Statistical models of environment-abundance relationships may be influenced by spatial autocorrelation in abundance, environmental variables, or both. Failure to account for spatial autocorrelation can lead to incorrect conclusions regarding both the absolute and relative importance of environmental variables as determinants of abundance. We consider several classes of statistical models that are appropriate for modeling environment-abundance relationships in the presence of spatial autocorrelation, and apply these to three case studies: 1) abundance of voles in relation to habitat characteristics; 2) a plant competition experiment; and 3) abundance of Orbatid mites along environmental gradients. We find that when spatial pattern is accounted for in the modeling process, conclusions about environmental control over abundance can change dramatically. We conclude with five lessons: 1) spatial models are easy to calculate with several of the most common statistical packages; 2) results from spatially-structured models may point to conclusions radically different from those suggested by a spatially independent model; 3) not all spatial autocorrelation in abundances results from spatial population dynamics; it may also result from abundance associations with environmental variables not included in the model; 4) the different spatial models do have different mechanistic interpretations in terms of ecological processes - thus ecological model selection should take primacy over statistical model selection; 5) the conclusions of the different spatial models are typically fairly similar - making any correction is more important than quibbling about which correction to make.},
-author = {Keitt, Timothy H. and Bj{\o}rnstad, Ottar N. and Dixon, Philip M. and Citron-Pousty, Steven},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Keitt et al. - 2002 - Accounting for Spatial Pattern When Modeling Organism-Environment Interactions.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {616--625},
-title = {{Accounting for Spatial Pattern When Modeling Organism-Environment Interactions}},
-url = {http://www.jstor.org/stable/3683664},
-volume = {25},
-year = {2002}
-}
-@article{Coleman1982,
-abstract = {Thorough censuses have been made of breeding birds on islands in Pymatuning Lake, a reservoir at the Pennsylvania—Ohio border. Analysis of the censuses yields the conclusion that for these islands the variation of the number of resident avian species with island size is that which one would expect if the birds were distributed randomly, with the probability of a breeding pair residing on an island proportional to the area of the island and independent of the presence of other pairs. This type of random placement of individuals can yield species—area relations which differ from those commonly employed for analysis of biogeographic data.},
-author = {Coleman, Bernard D. and Mares, Michael A. and Willig, Michael R. and Hsieh, Ying-Hen},
-doi = {10.2307/1937249},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coleman et al. - 1982 - Randomness, area, and species richness.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1121--1133},
-title = {{Randomness, area, and species richness}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1937249/full},
-volume = {63},
-year = {1982}
-}
-@article{Cornelissen2003,
-abstract = {There is growing recognition that classifying terrestrial plant species on the basis of their function (into 'functional types') rather than their higher taxonomic identity, is a promising way forward for tackling important ecological questions at the scale of ecosystems, landscapes or biomes. These questions include those on vegetation responses to and vegetation effects on, environmental changes (e.g. changes in climate, atmospheric chemistry, land use or other disturbances). There is also growing consensus about a shortlist of plant traits that should underlie such functional plant classifications, because they have strong predictive power of important ecosystem responses to environmental change and/or they themselves have strong impacts on ecosystem processes. The most favoured traits are those that are also relatively easy and inexpensive to measure for large numbers of plant species. Large international research efforts, promoted by the IGBP–GCTE Programme, are underway to screen predominant plant species in various ecosystems and biomes worldwide for such traits. This paper provides an international methodological protocol aimed at standardising this research effort, based on consensus among a broad group of scientists in this field. It features a practical handbook with step-by-step recipes, with relatively brief information about the ecological context, for 28 functional traits recognised as critical for tackling large-scale ecological questions.},
-author = {Cornelissen, Johannes H. C. and Lavorel, Sandra and Garnier, Eric and D{\'{i}}az, Sandra and Buchmann, Nina and Gurvich, D. E. and Reich, Peter B. and ter Steege, Hans and Morgan, H. D. and van der Heijden, M. G. A. and Pausas, J. G. and Poorter, Hendrik},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cornelissen et al. - 2003 - A handbook of protocols for standardised and easy measurement of plant functional traits worldwide.pdf:pdf},
-journal = {Australian Journal of Botany},
-number = {4},
-pages = {335--380},
-title = {{A handbook of protocols for standardised and easy measurement of plant functional traits worldwide}},
-volume = {51},
-year = {2003}
-}
-@article{Goffette-Nagot1999,
-author = {Goffette-Nagot, Florence and Schmitt, Bertrand},
-journal = {Environment and Planning A},
-number = {7},
-pages = {1239--1257},
-title = {{Agglomeration economies and spatial configurations in rural areas}},
-volume = {31},
-year = {1999}
-}
-@article{Faith1987,
-abstract = {The robustness of quantitative measures of compositional dissimilarity between sites was evaluated using extensive computer simulations of species' abundance patterns over one and two dimensional configurations of sample sites in ecological space. Robustness was equated with the strength over a range of models, of the linear and monotonic (rank-order) relationship between the compositional dissimilarities and the corresponding Euclidean distances between sites measured in the ecological space. The range of models reflected different assumptions about species' response curve shape, sampling pattern of sites, noise level of the data, species' interactions, trends in total site abundance, and beta diversity of gradients. The Kulczynski, Bray-Curtis and Relativized Manhattan measures were found to have not only a robust monotonic relationship with ecological distance, but also a robust linear (proportional) relationship until ecological distances became large. Less robust measures included Chord distance, Kendall's coefficient, Chisquared distance, Manhattan distance, and Euclidean distance. A new ordination method, hybrid multidimensional scaling (HMDS), is introduced that combines metric and nonmetric criteria, and so takes advantage of the particular properties of robust dissimilarity measures such as the Kulczynski measure.},
-author = {Faith, Daniel P. and Minchin, Peter R. and Belbin, Lee},
-doi = {10.1007/BF00038687},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faith, Minchin, Belbin - 1987 - Compositional dissimilarity as a robust measure of ecological distance.pdf:pdf},
-journal = {Vegetatio},
-number = {1-3},
-pages = {57--68},
-title = {{Compositional dissimilarity as a robust measure of ecological distance}},
-url = {http://link.springer.com/article/10.1007/BF00038687},
-volume = {69},
-year = {1987}
-}
-@article{Penfold1999a,
-abstract = {1 The relationship between the distribution of juveniles and conspecific trees was examined in a subtropical rain forest in south-east Queensland (Australia) to determine the role of compensatory mortality in maintaining the species richness of the forest. 2 Two species. which were among the most common canopy trees at the site, showed some evidence that the abundance of juveniles was reduced in the vicinity of conspecific trees. This spacing effect was particularly marked in Sloanea woollsii, but also present in Doryphora sassafras. The probability of finding juveniles of these species decreased as a function of (i) decreasing distance from the quadrats to the nearest conspecific tree and (ii) increasing density of conspecific trees (Sloanea woollsii only). In addition, these species accounted for a smaller proportion of the total number of juveniles close to conspecifics than they did at greater distances. 3 In contrast, the juveniles of a number of other species were more commonly found in the vicinity of conspecific trees. Two species had juveniles that were comparatively poorly dispersed: Acmena ingens and Polyosma cunninghamii juveniles were seldom found more than 10m and 15m away from conspecific trees. 4 Compensatory mortality might be necessary to prevent other species from being excluded by the two most common species, but it does not appear to be sufficient to explain how the majority of species co-exist with each other.},
-author = {Penfold, Guy C. and Lamb, David},
-doi = {10.1046/j.1365-2745.1999.00360.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {316--329},
-title = {{Species co-existence in an Australian subtropical rain forest: Evidence for compensatory mortality}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2745.1999.00360.x/full},
-volume = {87},
-year = {1999}
-}
-@article{Allison2012,
-abstract = {Trait-based models are an emerging tool in ecology with the potential to link community dynamics, environmental responses and ecosystem processes. These models represent complex communities by defining taxa with trait combinations derived from prior distributions that may be constrained by trade-offs. Herein I develop a model that links microbial community composition with physiological and enzymatic traits to predict litter decomposition rates. This approach allows for trade-offs among traits that represent alternative microbial strategies for resource acquisition. The model predicts that optimal strategies depend on the level of enzyme production in the whole community, which determines resource availability and decomposition rates. There is also evidence for facilitation and competition among microbial taxa that co-occur on decomposing litter. These interactions vary with community investment in extracellular enzyme production and the magnitude of trade-offs affecting enzyme biochemical traits. The model accounted for 69{\%} of the variation in decomposition rates of 15 Hawaiian litter types and up to 26{\%} of the variation in enzyme activities. By explicitly representing diversity, trait-based models can predict ecosystem processes based on functional trait distributions in a community. The model developed herein illustrates that traits influencing microbial enzyme production are some of the key controls on litter decomposition rates.},
-author = {Allison, S. D.},
-doi = {10.1111/j.1461-0248.2012.01807.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Allison - 2012 - A trait-based approach for modelling microbial litter decomposition.pdf:pdf},
-journal = {Ecology Letters},
-number = {9},
-pages = {1058--1070},
-title = {{A trait-based approach for modelling microbial litter decomposition}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2012.01807.x},
-volume = {15},
-year = {2012}
-}
-@article{Mori2005,
-abstract = {We propose a statistical index of industrial localization based on the Kullback-Leibler divergence. This index is particularly well suited to cases where industrial data are available only at the regional level. Unlike existing regional-level indices, our index can be employed to test the significance of industrial localization relative to a hypothesized reference distribution of probable locations across regions. In addition, one can test relative degrees of localization among industries. Finally, as with all Kullback-Leibler divergence indices, our index can be decomposed into components representing localization at various levels of spatial aggregation.},
-author = {Mori, Tomoya and Nishikimi, Koji and Smith, Tony E.},
-doi = {10.1162/003465305775098170},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mori, Nishikimi, Smith - 2005 - A Divergence Statistic for Industrial Localization.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {4},
-pages = {635--651},
-title = {{A Divergence Statistic for Industrial Localization}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/003465305775098170?journalCode=rest},
-volume = {87},
-year = {2005}
-}
-@incollection{Nissi2013,
-abstract = {Seismicity is a complex phenomenon and its statistical investigation is mainly concerned with the developing of computational models of earthquake processes. However, a substantial number of studies have been performed on the distribution of earthquakes in space and time in order to better understand the earthquake generation process and improve its prediction. The objective of the present paper, is to explore the effectiveness of a variant of Ripley's K-function, the M-function, as a new means of quantifying the clustering of earthquakes. In particular we test how the positions of epicentres are clustered in space with respect to their attributes values, i.e. the magnitude of the earthquakes. The strength of interaction between events is discussed and results for L'Aquila earthquake sequence are analysed.},
-author = {Nissi, Eugenia and Sarra, Annalina and Palermi, Sergio and Luca, Gaetano},
-booktitle = {Classification and Data Mining},
-chapter = {32},
-doi = {10.1007/978-3-642-28894-4_32},
-editor = {Giusti, Antonio and Ritter, Gunter and Vichi, Maurizio},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nissi et al. - 2013 - The Application of M-Function Analysis to the Geographical Distribution of Earthquake Sequence.pdf:pdf},
-isbn = {978-3-642-28893-7},
-language = {English},
-pages = {271--278},
-publisher = {Springer Berlin Heidelberg},
-title = {{The Application of M-Function Analysis to the Geographical Distribution of Earthquake Sequence}},
-url = {http://dx.doi.org/10.1007/978-3-642-28894-4{\_}32},
-year = {2013}
-}
-@article{Ricotta2012,
-abstract = {Aim Human activities have weakened biogeographical barriers to dispersal, increasing the rate of introduction of alien plants. However, their impact on beta diversity and floristic homogenization is poorly understood. Our goal is to compare the phylogenetic beta diversity of native species with that of two groups of alien species, archaeophytes and neophytes (introduced before and after ad1500, respectively), across European urban floras to explore how biological invasions affect phylogenetic turnover at a continental scale. Location Twenty European cities located in six countries between 49 and 53°N latitude in continental Europe and the British Isles. Methods To compare the phylogenetic beta diversity of native and alien species we use the average phylogenetic dissimilarity of individual floras from their group centroid in multivariate space. Differences in phylogenetic beta diversity among different species groups are then assessed using a randomization test for homogeneity of multivariate dispersions. Results Across European urban floras, and when contrasted with natives, archaeophytes are usually associated with lower levels of phylogenetic beta diversity while neophytes tend to increase phylogenetic differentiation. Main conclusions While archaeophytes tend to promote limited homogenization in phylogenetic beta diversity, because of their diverse geographical origin together with short residence times in the invaded regions, neophytes are not promoting biotic homogenization of urban floras across Europe. Therefore, in spite of the increasing rate of alien invasion, an intense phylogenetic homogenization of urban cities is not to be expected soon. {\textcopyright} 2011 Blackwell Publishing Ltd.},
-annote = {Cited By (since 1996):4
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: GEBIF
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Environmental Biology, University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo and {La Sorte}, Frank A. and Py{\v{s}}ek, Petr and Rapson, Gillian L. and Celesti-Grapow, Laura and Thompson, Ken},
-doi = {10.1111/j.1466-8238.2011.00715.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2012 - Phylogenetic beta diversity of native and alien species in European urban floras.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {7},
-pages = {751--759},
-title = {{Phylogenetic beta diversity of native and alien species in European urban floras}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84862307406{\&}partnerID=40{\&}md5=8facd0fa3c9afbca77ef0f5c4e2a2405},
-volume = {21},
-year = {2012}
-}
-@article{Perry2002,
-abstract = {This paper aims to provide guidance to ecologists with limited experience in spatial analysis to help in their choice of techniques. It uses examples to compare methods of spatial analysis for ecological field data. A taxonomy of different data types is presented, including point- and area-referenced data, with and without attributes. Spatially and non-spatially explicit data are distinguished. The effects of sampling and other transformations that convert one data type to another are discussed; the possible loss of spatial information is considered. Techniques for analyzing spatial pattern, developed in plant ecology, animal ecology, landscape ecology, geostatistics and applied statistics are reviewed briefly and their overlap in methodology and philosophy noted. the techniques are categorized according to their output and the inferences that may be drawn from them, in a discursive style without formulae. Methods are compared for four case studies with field data covering a range of types. These are: 1) percentage cover of three shrubs along a line transect; 2) locations and volume of a desert plant in a 1 ha area; 3) a remotely-sensed spectral index and elevation from 105 km2 of a mountainous region; and 4) land cover from three rangeland types within {\$}800\backslash {\{}\backslashrm km{\}}{\^{}}{\{}2{\}}{\$} of a coastal region. Initial approaches utilize mapping, frequency distributions and variance-mean indices. Analysis techniques we compare include: local quadrat variance, block quadrat variance, correlograms, variograms, angular correlation, directional variograms, wavelets, SADIE, nearest neighbour methods, Ripley's L̂(t), and various landscape ecology metrics. Our advice to ecologists is to use simple visualization techniques for initial analysis, and subsequently to select methods that are appropriate for the data type and that answer their specific questions of interest. It is usually prudent to employ several different techniques.},
-author = {Perry, Joe N. and Liebhold, A. M. and Rosenberg, Michael S. and Dungan, J. L. and Miriti, M. and Jakomulska, A. and Citron-Pousty, Steven},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Perry et al. - 2002 - Illustrations and Guidelines for Selecting Statistical Methods for Quantifying Spatial Pattern in Ecological Data.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {578--600},
-title = {{Illustrations and Guidelines for Selecting Statistical Methods for Quantifying Spatial Pattern in Ecological Data}},
-url = {http://www.jstor.org/stable/3683662},
-volume = {25},
-year = {2002}
-}
-@article{Guiasu2011,
-abstract = {The distribution of biodiversity at multiple sites of a region has been traditionally investigated through the additive partitioning of the regional biodiversity, called $\gamma$-diversity, into the average within-site biodiversity or $\alpha$-diversity, and the biodiversity among sites, or $\beta$-diversity. The standard additive partitioning of diversity requires the use of a measure of diversity which is a concave function of the relative abundance of species, like the Shannon entropy or the Gini- Simpson index, for instance. When a phylogenetic distance between species is also taken into account, Rao's quadratic index has been used as a measure of dissimilarity. Rao's index, however, is not a concave function of the distribution of relative abundance of either individual species or pairs of species and, consequently, only some nonstandard additive partitionings of diversity have been given using this index. The objective of this paper is to show that the weighted quadratic index of biodiversity, a generalization of the weighted Gini-Simpson index to the pairs of species, is a concave function of the joint distribution of the relative abundance of pairs of species and, therefore, may be used in the standard additive partitioning of diversity instead of Rao's index. The replication property of this new measure is also discussed.},
-author = {Guiasu, Radu Cornel and Guiasu, Silviu},
-doi = {10.4236/ns.2011.39104},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guiasu, Guiasu - 2011 - The weighted quadratic index of biodiversity for pairs of species a generalization of Rao's index.pdf:pdf},
-journal = {Natural Science},
-number = {9},
-pages = {795--801},
-title = {{The weighted quadratic index of biodiversity for pairs of species: a generalization of Rao's index}},
-url = {http://www.scirp.org/journal/PaperInformation.aspx?PaperID=7653},
-volume = {3},
-year = {2011}
-}
-@article{Zhang2013,
-abstract = {Zhang in 2012 introduced a nonparametric estimator of Shannon's entropy, whose bias decays exponentially fast when the alphabet is finite. We propose a methodology to estimate the bias of this estimator. We then use it to construct a new estimator of entropy. Simulation results suggest that this bias adjusted estimator has a significantly lower bias than many other commonly used estimators. We consider both the case when the alphabet is finite and when it is countably infinite.},
-annote = {Export Date: 25 March 2014
-Source: Scopus},
-author = {Zhang, Zhiyi and Grabchak, Michael},
-doi = {10.3390/e15061999},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Grabchak - 2013 - Bias adjustment for a nonparametric entropy estimator.pdf:pdf},
-journal = {Entropy},
-number = {6},
-pages = {1999--2011},
-title = {{Bias adjustment for a nonparametric entropy estimator}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84880017430{\&}partnerID=40{\&}md5=a57011706d4fd0da6ef57ead4dc4d95d},
-volume = {15},
-year = {2013}
-}
-@article{Jost2007,
-author = {Jost, Lou},
-doi = {10.1890/06-1736.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2007 - Partitioning diversity into independent alpha and beta components(2).pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2007 - Partitioning diversity into independent alpha and beta components.pdf:pdf},
-journal = {Ecology},
-number = {10},
-pages = {2427--2439},
-title = {{Partitioning diversity into independent alpha and beta components}},
-url = {http://www.esajournals.org/doi/abs/10.1890/06-1736.1},
-volume = {88},
-year = {2007}
-}
-@book{Gandrud2013,
-abstract = {Bringing together computational research tools in one accessible source, Reproducible Research with R and RStudio guides you in creating dynamic and highly reproducible research. Suitable for researchers in any quantitative empirical discipline, it presents practical tools for data collection, data analysis, and the presentation of results. With straightforward examples, the book takes you through a reproducible research workflow, showing you how to use: R for dynamic data gathering and automated results presentation knitr for combining statistical analysis and results into one document LaTeX for creating PDF articles and slide shows, and Markdown and HTML for presenting results on the web Cloud storage and versioning services that can store data, code, and presentation files; save previous versions of the files; and make the information widely available Unix-like shell programs for compiling large projects and converting documents from one markup language to another RStudio to tightly integrate reproducible research tools in one place Whether you're an advanced user or just getting started with tools such as R and LaTeX, this book saves you time searching for information and helps you successfully carry out computational research. It provides a practical reproducible research workflow that you can use to gather and analyze data as well as dynamically present results in print and on the web. Supplementary files used for the examples and a reproducible research project are available on the author's website.},
-author = {Gandrud, Christopher},
-edition = {2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gandrud - 2015 - Reproducible Research with R and R Studio.pdf:pdf},
-isbn = {146657285X},
-publisher = {Chapman and Hall/CRC},
-title = {{Reproducible Research with R and R Studio}},
-year = {2015}
-}
-@article{Scheiner2003,
-abstract = {Macroecological studies infer ecological processes based on observed patterns. An often used measure of pattern is the species-area curve. Insufficient attention has been paid to the variety of methods used to construct those curves. There are six different methods based on different combinations of: (1) the pattern of quadrats or areas sampled (nested, contiguous, noncontiguous, or island); (2) whether successively larger areas are constructed in a spatially explicit fashion or not; and (3) whether the curve is constructed from single values or mean values. The resulting six types of curves differ in their shapes, how diversity is encapsulated, and the scales encompassed. Inventory diversity ($\alpha$) can either represent a single value or a mean value, creating a difference in the focus of the measure. Differentiation diversity ($\beta$) can vary in the extent encompassed, and thus the spatial scale, depending on the pattern of quadrat placement. Species-area curves are used for a variety of purposes: extrapolation, setting a common grain, and hypothesis testing. The six types of curves differ in how they are used or interpreted in these contexts. A failure to recognize these differences can result in improper conclusions. Further work is needed to understand the sampling and measurement properties of the different types of species-area curves.},
-author = {Scheiner, Samuel M.},
-doi = {10.1046/j.1466-822X.2003.00061.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheiner - 2003 - Six types of species-area curves.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {6},
-pages = {441--447},
-title = {{Six types of species-area curves}},
-url = {http://dx.doi.org/10.1046/j.1466-822X.2003.00061.x},
-volume = {12},
-year = {2003}
-}
-@book{Dobzhansky1937,
-address = {New York},
-author = {Dobzhansky, T.},
-isbn = {0-231-05475-0},
-publisher = {Columbia University Press},
-title = {{Genetics and the Origin of Species}},
-url = {http://en.wikipedia.org/wiki/Genetics{\_}and{\_}the{\_}Origin{\_}of{\_}Species},
-year = {1937}
-}
-@article{DiBattista2016,
-abstract = {This paper presents the R package BioFTF, which is a tool for statistical biodiversity assessment in the functional data analysis framework. Diversity is a key topic in many research fields; however, in the literature, it is demonstrated that the existing indices do not capture the different aspects of this concept. Thus, a main drawback is that different indicators may lead to different orderings among communities according to their biodiversity. A possible method to evaluate biodiversity consists in using diversity profiles that are curves depending on a specific parameter. In this setting, it is possible to adopt some functional instruments proposed in the literature, such as the first and second derivatives, the curvature, the radius of curvature and the arc length. Specifically, the derivatives and the curvature (or the radius of curvature) highlight any peculiar behaviour of the profiles, whereas the arc length helps in ranking curves, given the richness. Because these instruments do not solve the issue of ranking communities with different numbers of species, we propose an important methodological contribution that introduces the surface area. Indeed, this tool is a scalar measure that reflects the information provided by the biodiversity profile and allows for ordering communities with different richness. However, this approach requires mathematical skills that the average user may not have; thus, our idea is to provide a user-friendly tool for both non-statistician and statistician practitioners to measure biodiversity in a functional context.},
-author = {{Di Battista}, Tonio and Fortuna, F. and Maturo, Fabrizio},
-doi = {10.1016/j.ecolind.2016.10.032},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Di Battista, Fortuna, Maturo - 2016 - BioFTF An R package for biodiversity assessment with the functional data analysis approach.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {726--732},
-title = {{BioFTF: An R package for biodiversity assessment with the functional data analysis approach}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X16306252},
-volume = {73},
-year = {2017}
-}
-@article{Box1958,
-author = {Box, G. E. P. and Muller, Mervin E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Box, Muller - 1958 - A Note on the Generation of Random Normal Deviates.pdf:pdf},
-journal = {The Annals of Mathematical Statistics},
-number = {2},
-pages = {610--611},
-title = {{A Note on the Generation of Random Normal Deviates}},
-url = {http://www.jstor.org/stable/2237361},
-volume = {29},
-year = {1958}
-}
-@article{Blonder2017,
-abstract = {Hutchinson's n -dimensional hypervolume concept for the interpretation of niches as geometric shapes has provided a foundation for research across different fields of ecology and evolution. There is now an expanding set of applications for hypervolume concepts, as well as a growing set of statistical methods available to operationalize this concept with data. The concept has been applied to environmental, resource, functional trait, and morphometric axes and to different scales, i.e. from individuals, species, to communities and clades. Further, these shapes have been variously interpreted as niches, ecological or evolutionary strategy spaces, or proxies for community structure. This paper highlights these applications' shared mathematical framework, surveys uses of the hypervolume concept across fields, discusses key limitations and assumptions of hypervolume concepts in general, provides a critical guide to available statistical estimation methods, and delineates the situations where hypervolume concepts can be useful.},
-author = {Blonder, Benjamin},
-doi = {10.1111/ecog.03187},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blonder-2017-Ecography.pdf:pdf},
-issn = {16000587},
-journal = {Ecography},
-title = {{Hypervolume concepts in niche- and trait-based ecology}},
-volume = {in press},
-year = {2017}
-}
-@article{VanBuuren2011,
-abstract = {The R package mice imputes incomplete multivariate data by chained equations. The software mice 1.0 appeared in the year 2000 as an S-PLUS library, and in 2001 as an R package. mice 1.0 introduced predictor selection, passive imputation and automatic pooling. This article documents mice 2.9, which extends the functionality of mice 1.0 in several ways. In mice 2.9, the analysis of imputed data is made completely general, whereas the range ofmodels under which pooling works is substantially extended. mice 2.9 adds new functionality for imputing multilevel data, automatic predictor selection, data handling, post-processing imputed values, specialized pooling routines, model selection tools, and diagnostic graphs. Imputation of categorical data is improved in order to bypass problems caused by perfect prediction. Special attention is paid to transformations, sum scores, indices and interactions using passive imputation, and to the proper setup of the predictor matrix. mice 2.9 can be downloaded from the Comprehensive R Archive Network. This article provides a hands-on, stepwise approach to solve applied incomplete data problems. Keywords:},
-author = {van Buuren, Stef and Groothuis-Oudshoorn, Karin},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/van Buuren, Groothuis-Oudshoorn - 2011 - mice Multivariate Imputation by Chained Equations in R.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {3},
-pages = {1--67},
-title = {{mice: Multivariate Imputation by Chained Equations in R}},
-volume = {45},
-year = {2011}
-}
-@phdthesis{Heuret2002,
-author = {Heuret, Patrick},
-publisher = {Universit{\'{e}} de Nancy I},
-title = {{Analyse et mod{\'{e}}lisation de s{\'{e}}quences d'{\'{e}}v{\'{e}}nements botaniques : application {\`{a}} la compr{\'{e}}hension des processus de croissance, de ramification et de floraison}},
-year = {2002}
-}
-@article{Chapin2000,
-abstract = {Human alteration of the global environment has triggered the sixth major extinction event in the history of life and caused widespread changes in the global distribution of organisms. These changes in biodiversity alter ecosystem processes and change the resilience of ecosystems to environmental change. This has profound consequences for services that humans derive from ecosystems. The large ecological and societal consequences of changing biodiversity should be minimized to preserve options for future solutions to global environmental problems.},
-author = {Chapin, F. Stuart III and Zavaleta, Erika S. and Eviner, Valerie T. and Naylor, Rosamond L. and Vitousek, Peter M. and Reynolds, Heather L. and Hooper, David U. and Lavorel, Sandra and Sala, Osvaldo E. and Hobbie, Sarah E. and Mack, Michelle C. and D{\'{i}}az, Sandra},
-doi = {10.1038/35012241},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chapin et al. - 2000 - Consequences of changing biodiversity.pdf:pdf},
-journal = {Nature},
-number = {6783},
-pages = {234--242},
-title = {{Consequences of changing biodiversity}},
-url = {http://www.nature.com/nature/journal/v405/n6783/full/405234a0.html},
-volume = {405},
-year = {2000}
-}
-@article{DeBenedictis1973,
-author = {DeBenedictis, Paul A.},
-doi = {10.2307/2459799},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/DeBenedictis - 1973 - On the Correlations between Certain Diversity Indices.pdf:pdf},
-journal = {The American Naturalist},
-number = {954},
-pages = {295--302},
-title = {{On the Correlations between Certain Diversity Indices}},
-volume = {107},
-year = {1973}
-}
-@article{Couteron2004,
-author = {Couteron, Pierre and P{\'{e}}lissier, Rapha{\"{e}}l},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Couteron, P{\'{e}}lissier - 2004 - Additive apportioning of species diversity towards more sophisticated models and analyses.pdf:pdf},
-journal = {Oikos},
-keywords = {Couteron (2004).pdf},
-mendeley-tags = {Couteron (2004).pdf},
-number = {1},
-pages = {215--221},
-title = {{Additive apportioning of species diversity: towards more sophisticated models and analyses}},
-volume = {107},
-year = {2004}
-}
-@article{Shimadzu2015,
-abstract = {Range migrations in response to climate change, invasive species and the emergence of novel ecosystems highlight the importance of temporal turnover in community composition as a fundamental part of global change in the Anthropocene. Temporal turnover is usually quantified using a variety of metrics initially developed to capture spatial change. However, temporal turnover is the consequence of unidirectional community dynamics resulting from processes such as population growth, colonisation and local extinction. Here, we develop a framework based on community dynamics and propose a new temporal turnover measure. A simulation study and an analysis of an estuarine fish community both clearly demonstrate that our proposed turnover measure offers additional insights relative to spatial context-based metrics. Our approach reveals whether community turnover is due to shifts in community composition or in community abundance and identifies the species and/or environmental factors that are responsible for any change.},
-annote = {Erreur dans le calcul de lambda(t+h): lambda{\_}i(t) ne peut pas {\^{e}}tre sorti de l'int{\'{e}}grale : il n'est pas constant.
-La relation de l'{\'{e}}quation 2 ne tient pas.},
-author = {Shimadzu, Hideyasu and Dornelas, Maria and Magurran, Anne E.},
-doi = {10.1111/2041-210X.12438},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shimadzu, Dornelas, Magurran - 2015 - Measuring temporal turnover in ecological communities.pdf:pdf},
-issn = {2041210X},
-journal = {Methods in Ecology and Evolution},
-number = {12},
-pages = {1384--1394},
-title = {{Measuring temporal turnover in ecological communities}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12438},
-volume = {6},
-year = {2015}
-}
-@incollection{Diggle1976,
-address = {London},
-author = {Diggle, Peter J.},
-booktitle = {Spatial Analysis in Archaeology},
-editor = {Hodder, I and Orton, C},
-publisher = {Cambridge University Press},
-title = {{Note on the Clark and Evans test of spatial randomness}},
-year = {1976}
-}
-@misc{Foley2007,
-abstract = {he Amazon Basin is one of the world's most important bioregions, harboring a rich array of plant and animal species and offering a wealth of goods and services to society. For years, ecological science has shown how large scale forest clearings cause declines in biodiversity and the availability of forest products. Yet some important changes in the rainforests, and in the ecosystem services they provide, have been underappreciated until recently. Emerging research indicates that land use in the Amazon goes far beyond clearing large areas of forest; selective logging and other canopy damage is much more pervasive than once believed. Deforestation causes collateral damage to the surrounding forests - through enhanced drying of the forest floor, increased frequency of fires, and lowered productivity. The loss of healthy forests can degrade key ecosystem services, such as carbon storage in biomass and soils, the regulation of water balance and river flow, the modulation of regional climate patterns, and the amelioration of infectious diseases. We review these newly revealed changes in the Amazon rainforests and the ecosystem services that they provide.},
-author = {Foley, Jonathan A. and Asner, Gregory P. and Costa, Marcos Heil and Coe, Michael T. and DeFries, Ruth and Gibbs, Holly K. and Howard, Erica A. and Olson, Sarah and Patz, Jonathan and Ramankutty, Navin and Snyder, Peter},
-booktitle = {Frontiers in Ecology and the Environment},
-doi = {10.1890/1540-9295(2007)5[25:ARFDAL]2.0.CO;2},
-isbn = {1540-9295},
-issn = {15409295},
-number = {1},
-pages = {25--32},
-title = {{Amazonia revealed: Forest degradation and loss of ecosystem goods and services in the Amazon Basin}},
-volume = {5},
-year = {2007}
-}
-@article{Bormann1953,
-author = {Bormann, F. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bormann - 1953 - The Statistical Efficiency of Sample Plot Size and Shape in Forest Ecology Author.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {474--487},
-title = {{The Statistical Efficiency of Sample Plot Size and Shape in Forest Ecology Author}},
-volume = {34},
-year = {1953}
-}
-@article{Diaz2001,
-abstract = {The study of central corneal endothelium morphology is important in Ophthalmology. Some of the pathologies that could compromise endothelial cell morphology are trauma, cataract, surgery, use of contact lenses, corneal dystrophies or degenerations. The quantitative analysis of cell shape and cellular pattern is more sensitive in detecting subtle changes in endothelial morphology than cell density measurement or cell area analysis. In this paper, the morphology of the central cornea, the most important area from the point of view of vision, is studied through an associated bivariate spatial point pattern: the centroids of the cells and the triple points, that is, the points where three different cells converge. Nine different summary descriptors (widely used in the statistical analysis of spatial point patterns) have been used: the empty space distribution function; the nearest neighbour distribution function and Ripley's K-function for each type of point separately (centroids and triple points), plus the corresponding three versions of these functions in the bivariate case. A control sample with similar age and cell density and no known abnormality is associated to each patient. The above descriptors are calculated for the patient and the controls. Each descriptive of the patient is compared with the corresponding descriptors from the controls by means of a graphical analysis and a formal test. Some patients presenting different pathologies are analysed in detail. Endothelia considered morphologically abnormal by visual inspection, which were not detected by hexagonality or density analysis, could be distinguished from control endothelia by these new descriptors. Copyright (C) 2001 John Wiley {\&} Sons, Ltd.},
-annote = {Article
-English
-STAT MED
-495AV},
-author = {D{\'{i}}az, M. E. and Ayala, G. and Quesada, S. and Martinez-Costa, L.},
-doi = {10.1002/sim.931},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diaz et al. - 2001 - Testing abnormality in the spatial arrangement of cells in the corneal endothelium using spatial point processes.pdf:pdf},
-journal = {Statistics in Medicine},
-number = {22},
-pages = {3429--3439},
-title = {{Testing abnormality in the spatial arrangement of cells in the corneal endothelium using spatial point processes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.931/abstract},
-volume = {20},
-year = {2001}
-}
-@techreport{Degen1999,
-address = {Kourou},
-author = {Degen, Bernd},
-publisher = {Silvolab},
-title = {{Dendrobase : Genetic system of tropical tree species}},
-year = {1999}
-}
-@article{Witting2000,
-abstract = {The relationship between Fisher's fundamental theorem of natural selection and the ecological environment of density regulation is examined. Using a linear model, it is shown that the theorem holds when density regulation is caused by exploitative competition and that the theorem fails with interference competition. In the latter case the theorem holds only at the limit of zero population density and/or at the limit where the competitively superior individuals cannot monopolise the resource. The results are discussed in relation to population dynamics and life history evolution, where evidence suggests that the level of interference competition in natural populations is so high that the fundamental theorem does not apply.},
-author = {Witting, Lars},
-doi = {10.1023/a:1002788313345},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Witting - 2000 - Interference Competition Set Limits to the Fundamental Theorem of Natural Selection.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {2},
-pages = {107--120},
-title = {{Interference Competition Set Limits to the Fundamental Theorem of Natural Selection}},
-url = {http://dx.doi.org/10.1023/A{\%}3A1002788313345},
-volume = {48},
-year = {2000}
-}
-@article{DeBello2010,
-abstract = {A methodology for partitioning of biodiversity into a, b and g components has long been debated, resulting in different mathematical frameworks. Recently, use of the Rao quadratic entropy index has been advocated since it allows comparison of various facets of diversity (e.g. taxonomic, phyloge- netic and functional) within the same mathema- tical framework. However, if not well implemented, the Rao index can easily yield biologically meaning- less results and lead into a mathematical labyrinth. As a practical guideline for ecologists, we present a critical synthesis of diverging implementations of the index in the recent literature and a new extension of the index for measuring b-diversity. First, we detail correct computation of the index that needs to be applied in order not to obtain negative b-diversity values, which are ecologically unaccep- table, and elucidate the main approaches to calculate the Rao quadratic entropy at different spatial scales. Then, we emphasize that, similar to other entropy measures, the Rao index often pro- duces lower-than-expected b-diversity values. To solve this, we extend a correction based on equiva- lent numbers, as proposed by Jost (2007), to the Rao index. We further show that this correction can be applied to additive partitioning of diversity and not only its multiplicative form. These developments around around the Rao index open up an exciting avenue to develop an estimator of turnover diversity across different environmental and temporal scales, allow- ing meaningful comparisons of partitioning across species, phylogenetic and functional diversities within the same mathematical framework. We also propose a set of R functions, based on existing developments,which performdifferent key computa- tions to apply this framework in biodiversity science.},
-author = {de Bello, Francesco and Lavergne, S{\'{e}}bastien and Meynard, Christine N. and Lep{\v{s}}, Jan and Thuiller, Wilfried},
-doi = {10.1111/j.1654-1103.2010.01195.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Bello et al. - 2010 - The partitioning of diversity showing Theseus a way out of the labyrinth.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {992--1000},
-title = {{The partitioning of diversity: showing Theseus a way out of the labyrinth}},
-url = {http://dx.doi.org/10.1111/j.1654-1103.2010.01195.x},
-volume = {21},
-year = {2010}
-}
-@article{Ricotta2004a,
-abstract = {Most ecological diversity indices summarize the information about the relative abundances of species without reflecting taxonomic differences between species. Nevertheless, in environmental conservation practice, data on species abundances are mostly irrelevant and generally unknown. In such cases, to summarize the conservation value of a given site, so-called 'taxonomic diversity' measures can be used. Such measures are based on taxonomic relations among species and ignore species relative abundances. In this paper, bridging the gap between traditional biodiversity measures and taxonomic diversity measures, I introduce a parametric diversity index that combines species relative abundances with their taxonomic distinctiveness. Due to the parametric nature of the proposed index, the contribution of rare and abundant species to each diversity measure is explicit.},
-author = {Ricotta, Carlo},
-doi = {10.1111/j.1366-9516.2004.00069.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2004 - A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species(2).pdf:pdf},
-journal = {Diversity and Distributions},
-number = {2},
-pages = {143--146},
-title = {{A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1366-9516.2004.00069.x/full},
-volume = {10},
-year = {2004}
-}
-@article{Goreaud2002,
-abstract = {Recent changes in forestry practices raise new scientific issues concerning the dynamics of mixed forests, and especially the coexistence of different species. The spatial structure of such forest stands is known to play a key role in their dynamics, but classical forest models are not adapted to study this phenomenon. Foresters have therefore begun to build distance-dependent individual-based forest models. As far as theoretical models are concerned, the relation between competition and the coexistence of various plant species in a mixed community has been studied extensively in theoretical ecology, but few of the corresponding models explicitly take the spatial structure of the community into account. The aim of this paper is to present a simple individual-based mechanistic model of neighbourhood competition that allows to study the relation between the spatial structure of mixed stands and the survival of an inferior competitor. We have build this model as an extension of former theoretical models of competition for a soil resource, by adding explicit spatial interactions. We have studied it both analytically and through simulations, using generalised Gibbs processes to simulate stands of various spatial structures. At the individual scale, we have obtained an explicit relation between the survival of a tree, the specific composition of its neighbourhood, and soil fertility. At the stand scale, we have linked the number of surviving trees to the spatial structure, and shown how interspecific repulsion and aggregated patterns improve the survival of inferior competitors. We have also illustrated how the competition process modifies the spatial structure of the stand. Such a neighbourhood competition model is thus a useful tool to study the relation between the spatial structure of a community and its dynamics.},
-author = {Goreaud, Fran{\c{c}}ois and Loreau, Michel and Millier, Claude},
-doi = {10.1016/S0304-3800(02)00058-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Goreaud, Loreau, Millier - 2002 - Spatial structure and the survival of an inferior competitor a theoretical model of neighbourhood comp.pdf:pdf},
-journal = {Ecological Modelling},
-number = {1-2},
-pages = {1--19},
-title = {{Spatial structure and the survival of an inferior competitor: a theoretical model of neighbourhood competition in plants}},
-url = {http://www.sciencedirect.com/science/article/pii/S0304380002000583},
-volume = {158},
-year = {2002}
-}
-@article{Anderson2011,
-abstract = {A recent increase in studies of $\beta$ diversity has yielded a confusing array of concepts, measures and methods. Here, we provide a roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements. We distinguish two types of $\beta$ diversity: directional turnover along a gradient vs. non-directional variation. Different measures emphasize different properties of ecological data. Such properties include the degree of emphasis on presence/absence vs. relative abundance information and the inclusion vs. exclusion of joint absences. Judicious use of multiple measures in concert can uncover the underlying nature of patterns in $\beta$ diversity for a given dataset. A case study of Indonesian coral assemblages shows the utility of a multi-faceted approach. We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in $\beta$ diversity.},
-author = {Anderson, Marti J. and Crist, Thomas O. and Chase, Jonathan M. and Vellend, Mark and Inouye, Brian D. and Freestone, Amy L. and Sanders, Nathan J. and Cornell, Howard V. and Comita, Liza S. and Davies, Kendi F. and Harrison, Susan P. and Kraft, Nathan J. B. and Stegen, James C. and Swenson, Nathan G.},
-doi = {10.1111/j.1461-0248.2010.01552.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anderson et al. - 2011 - Navigating the multiple meanings of $\beta$ diversity a roadmap for the practicing ecologist.pdf:pdf},
-journal = {Ecology Letters},
-number = {1},
-pages = {19--28},
-title = {{Navigating the multiple meanings of $\beta$ diversity: a roadmap for the practicing ecologist}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2010.01552.x},
-volume = {14},
-year = {2011}
-}
-@article{Gao2015,
-abstract = {Aggregation of species on the basis of their trophic relationships is a fundamental step for quantifying, visualizing and thereby uncovering the structure of food webs. Although the Additive Jaccard Similarity (AJS) has been widely used to measure trophic similarity between species, it has also been criticized for its limited ability to find species with equivalent trophic roles, especially when they do not share the same predators and prey. In this study, we proposed a new trophic similarity measure, the Extended Additive Jaccard Similarity (EAJS), which quantifies trophic similarity between species based not only on the similarity of their shared predators and prey at adjacent trophic levels but at all trophic levels throughout a food web. Average linkage clustering was then used to aggregate species in the mammalian food web for the Serengeti ecosystem in northern Tanzania and southern Kenya on the basis of both trophic similarity measures.Compared to groups identified on the basis of AJS values, groups derived using EAJS had greater within-group similarity in terms of species' trophic relationships and greater discrimination vs. those in other groups. Groups based on EAJS values also better reflected ecological factors known to structure food webs, including producer-level habitat segregation and mammalian body mass. The advantage of EAJS lies in the fact that it is designed to consider species feeding relations in food webs that is not limited to adjacent trophic levels. Our approach provides a means for revealing the patterns of trophic relations among species in food webs and exploring known and unknown factors shaping food web structure.},
-author = {Gao, Peng and Kupfer, John A.},
-doi = {10.1016/j.ecoinf.2015.09.013},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gao - 2013 - Detecting spatial aggregation from distance sampling a probability distribution model of nearest neighbor distance.pdf:pdf},
-journal = {Ecological Informatics},
-pages = {110--118},
-title = {{Uncovering food web structure using a novel trophic similarity measure}},
-url = {http://dx.doi.org/10.1016/j.ecoinf.2015.09.013},
-volume = {30},
-year = {2015}
-}
-@article{Lagache2013,
-abstract = {One major question in molecular biology is whether the spatial distribution of observed molecules is random or organized in clusters. Indeed, this analysis gives information about molecules' interactions and physical interplay with their environment. The standard tool for analyzing molecules' distribution statistically is the Ripley's K function, which tests spatial randomness through the computation of its critical quantiles. However, quantiles' computation is very cumbersome, hindering its use. Here, we present an analytical expression of these quantiles, leading to a fast and robust statistical test, and we derive the characteristic clusters' size from the maxima of the Ripley's K function. Subsequently, we analyze the spatial organization of endocytic spots at the cell membrane and we report that clathrin spots are randomly distributed while clathrin-independent spots are organized in clusters with a radius of , which suggests distinct physical mechanisms and cellular functions for each pathway.},
-author = {Lagache, Thibault and Lang, Gabriel and Sauvonnet, Nathalie and Olivo-Marin, Jean-Christophe},
-doi = {10.1371/journal.pone.0080914},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lagache et al. - 2013 - Analysis of the Spatial Organization of Molecules with Robust Statistics(2).pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lagache et al. - 2013 - Analysis of the Spatial Organization of Molecules with Robust Statistics.pdf:pdf},
-journal = {Plos One},
-number = {12},
-pages = {e80914},
-title = {{Analysis of the Spatial Organization of Molecules with Robust Statistics}},
-url = {http://dx.doi.org/10.1371{\%}2Fjournal.pone.0080914},
-volume = {8},
-year = {2013}
-}
-@article{Bernstein1997,
-abstract = {This paper estimates the effects of intranational and international R{\&}D spillovers on the cost and production structure for ten Canadian and Japanese manufacturing industries. Domestic spillovers generate greater effects on average variable cost and factor intensities compared with international spillovers between the two countries. Private and social rates of return to R{\&}D are calculated for each industry in both countries. Social rates of return to R{\&}D are one and one-half to twelve times the private returns. The Canadian social rates of return are generally two to three times higher than the Japanese rates.},
-author = {Bernstein, Jeffrey I. and Yan, Xiaoyi},
-doi = {10.2307/136339},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bernstein, Yan - 1997 - International R{\&}D Spillovers between Canadian and Japanese Industries.pdf:pdf},
-journal = {The Canadian Journal of Economics},
-number = {2},
-pages = {276--294},
-title = {{International R{\&}D Spillovers between Canadian and Japanese Industries}},
-url = {https://www.jstor.org/stable/136339},
-volume = {30},
-year = {1997}
-}
-@article{Leemans1991,
-abstract = {The spatial pattern of seedlings, saplings and canopy trees was studied in two spruce (Picea abies) forests in central Sweden during the period 1984-88. Canopy and forest structure were determined in five 0.25-ha plots. Life stage classes were distinguished on the basis of age and size distributions. Ripley's K-function (1977) was used to analyse the spatial patterns within each class. A random distribution of seedlings was replaced by a more aggregated pattern on a small scale during the establishment phase. Saplings and sub-canopy trees were strongly aggregated and canopy trees were randomly distributed within the plots. The proportion of individuals growing in gaps was used as an index of association between the spatial pattern in saplings and sub-canopy trees and the occurrence of small (50-350 m2) canopy gaps. Under the null hypothesis of independence, the expected value of this statistic would equal the canopy gap ratio for the stand. Monte Carlo simulation of this statistic, using fixed sapling positions and randomly repositioned canopy gaps, confirmed the importance of canopy gaps for the final success of establishment of spruce. The association of understorey trees with gaps suggest that small gaps are typically closed by recruitment of new saplings from a sapling bank rather than by the release of larger suppressed trees.},
-author = {Leemans, R.},
-doi = {10.1007/BF00033209},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leemans - 1991 - Canopy gaps and establishment patterns of spruce (Picea abies (L.) Karst.) in two old-growth coniferous forests in cent.pdf:pdf},
-journal = {Vegetatio},
-number = {2},
-pages = {157--165},
-title = {{Canopy gaps and establishment patterns of spruce (Picea abies (L.) Karst.) in two old-growth coniferous forests in central Sweden}},
-url = {https://link.springer.com/article/10.1007/BF00033209},
-volume = {93},
-year = {1991}
-}
-@article{Anselin2000,
-abstract = {This paper implements a novel approach to formalizing spatial externalities by employing spatial econometric methods that combine spatial dependence and spatial heterogeneity in the form of spatial regimes. The results confirm earlier findings that academic externalities are not uniform across sectors but also indicate important differences across sectors in terms of agglomeration effects.},
-author = {Anselin, Luc and Varga, Attila and Acs, Zoltan J.},
-doi = {10.1111/j.1435-5597.2000.tb01766.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anselin, Varga, Acs - 2000 - Geographic and sectoral characteristics of academic knowledge externalities.pdf:pdf},
-journal = {Papers in Regional Science},
-number = {4},
-pages = {435--443},
-title = {{Geographic and sectoral characteristics of academic knowledge externalities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1435-5597.2000.tb01766.x/abstract},
-volume = {79},
-year = {2000}
-}
-@article{Schooley2001,
-abstract = {Burrowing mammals create disturbances that increase the ecological heterogeneity of landscapes. In desert systems, banner-tailed kangaroo rats (Dipodomys spectabilis) construct large mounds that greatly influence the spatial patterning of soils, plants, and animals. The overall effects of the patches generated by D. spectabilis depend on the dispersion patterns of the mounds; these patterns may be sensitive to scale and landscape position. We examined the distribution of D. spectabilis mounds across multiple scales in four 40-ha grassland plots in New Mexico, USA, between 14 September and 7 November 1997. We used Ripley's K-function for our point- pattern analysis. The dispersion patterns of mounds were generally scale-sensitive but depended somewhat on plot-level densities, which were related to topographic position and grazing history. Mound spacing was either regular or random at small scales (0-50 m), random or aggregated at intermediate scales (50-300 m), and aggregated at large scales (300-3000 m). This scale-dependency of pattern reflected spatial domains in which different biotic (territoriality, dispersal, grazing) and abiotic (soil texture and drainage) factors exerted strong influences. How other organisms perceive the spatial patterning of mounds will depend on the extent of their movements. Patches may appear regular to one species but aggregated to another. The dispersion of D. spectabilis mounds also has implications for the spatial structuring of desert rodent communities. D. spectabilis excludes smaller species of kangaroo rats from areas around their mounds; they create spatial heterogeneity in behavioural dominance that may influence the distribution of subordinate species at multiple scales.},
-author = {Schooley, Robert L and Wiens, John A},
-doi = {10.1023/A:1011122218548},
-journal = {Landscape Ecology},
-number = {3},
-pages = {267--277},
-title = {{Dispersion of kangaroo rat mounds at multiple scales in New Mexico, USA}},
-url = {https://link.springer.com/article/10.1023/A:1011122218548},
-volume = {16},
-year = {2001}
-}
-@book{Arbia1989,
-address = {Dordrecht},
-author = {Arbia, Giuseppe},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia - 1989 - Spatial Data Configuration in Statistical Analysis of Regional Economic and Related Problems.pdf:pdf},
-keywords = {MAUP},
-publisher = {Kluwer},
-title = {{Spatial Data Configuration in Statistical Analysis of Regional Economic and Related Problems}},
-year = {1989}
-}
-@article{Nekola1999,
-abstract = {Aim Our aim was to understand how similarity changes with distance in biological communities, to use the distance decay perspective as quantitative technique to describe biogeographic pattern, and to explore whether growth form, dispersal type, rarity, or support affected the rate of distance decay in similarity. Location North American spruce-fir forests, Appalachian montane spruce-fir forests. Methods We estimated rates of distance decay through regression of log-transformed compositional similarity against distance for pairwise comparisons of thirty-four white spruce plots and twenty-six black spruce plots distributed from eastern Canada to Alaska, six regional floras along the crest of the Appalachians, and six regional floras along the east–west extent of the boreal forest. Results Similarity decreased significantly with distance, with the most linear models relating the log of similarity to untransformed distance. The rate of similarity decay was 1.5–1.9 times higher for vascular plants than for bryophytes. The rate of distance decay was highest for berry-fruited and nut-bearing species (1.7 times higher than plumose-seeded species and 1.9 times higher than microseeded/spore species) and 2.1 times higher for herbs than woody plants. There was no distance decay for rare species, while species of intermediate frequency had 2.0 times higher distance decay rates than common species. The rate of distance decay was 2.7 times higher for floras from the fragmented Appalachians than for floras from the contiguous boreal forest. Main conclusions The distance decay of similarity can be caused by either a decrease in environmental similarity with distance (e.g. climatic gradients) or by limits to dispersal and niche width differences among taxa. Regardless of cause, the distance decay of similarity provides a simple descriptor of how biological diversity is distributed and therefore has consequences for conservation strategy.},
-author = {Nekola, Jeffrey C. and White, Peter S.},
-doi = {10.1046/j.1365-2699.1999.00305.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nekola, White - 1999 - The Distance Decay of Similarity in Biogeography and Ecology.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {4},
-pages = {867--878},
-title = {{The Distance Decay of Similarity in Biogeography and Ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2699.1999.00305.x/abstract},
-volume = {26},
-year = {1999}
-}
-@article{Dray2014,
-abstract = {The use of next-gen sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and(or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene datasets.},
-author = {Dray, St{\'{e}}phane and Pavoine, Sandrine and de C{\'{a}}rcer, D. Aguirre},
-doi = {10.1111/1755-0998.12300},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dray, Pavoine, de C{\'{a}}rcer - 2014 - Considering external information to improve the phylogenetic comparison of microbial communities a new.pdf:pdf},
-issn = {1755098X},
-journal = {Molecular Ecology Resources},
-month = {jun},
-number = {2},
-pages = {242--249},
-title = {{Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)}},
-url = {http://doi.wiley.com/10.1111/1755-0998.12300},
-volume = {15},
-year = {2014}
-}
-@article{Bonneu2007,
-abstract = {We examine a database of fire department emergencies in the surroundings of the city of Toulouse during the year 2004, using methods of statistical analysis for spatial point patterns. Firemen emergencies are characterized by their positions and different features (time, duration, type,{\ldots}) that one can model as a spatio-temporal marked point process. For our study, we consider the following characteristics of firemen emergencies: positions, time of occurrences and marks which take into account the duration and the number of firemen involved. We use graphical methods to explore the structure of the underlying spatial point process with a final objective of choosing a suitable model for future work. We first review the basic concepts and methods used in the paper. Considering the marginal spatio-temporal point pattern, we propose to evaluate the importance of the variation of intensity over time in comparison with spatial variation and to test the dependence between positions and time. Afterwards, we conduct an exploratory analysis of the marks to test their dependence with positions as well as their dependence with time. Our resulting framework of independence allows us to explore the dependence between categories in order to test the random labeling hypothesis. Then, under the hypothesis of random labeling and invariance in time which have been established in the first two parts, we fit a spatial point process model to the unmarked spatial point pattern aggregated over the whole year. Finally, we analyze the goodness-of-fit of our models by exploring the first and second order characteristics of simulations from the fitted models. Throughout this article, the exploratory analysis is made using mainly the R package spatstat. An exposure to point processes is useful but not indispensable for understanding the exposition.},
-author = {Bonneu, Florent},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonneu - 2007 - Exploring and Modeling Fire Department Emergencies with a Spatio-Temporal Marked Point Process.pdf:pdf},
-journal = {Case Studies in Business, Industry and Government Statistics},
-number = {2},
-pages = {139--152},
-title = {{Exploring and Modeling Fire Department Emergencies with a Spatio-Temporal Marked Point Process}},
-url = {http://journal-sfds.fr/index.php/csbigs/article/view/376/356},
-volume = {1},
-year = {2007}
-}
-@article{Ricotta2009b,
-abstract = {Jost (Ecology, 88:2427-2439, 2007) recently showed that the Shannon diversity is the only standard diversity measure that can be partitioned into meaningful independent alpha and beta components when plot weights are unequal. This conclusion is very disappointing if one wants to calculate the beta diversity of unequal weighted plots using a parametric measure with varying sensitivities to the occurrence of rare and abundant species. To overcome this impasse, at least partially, in this paper, I propose a parametric measure of beta diversity that is based on the combination of Shannon's entropy with Hurlbert's 'expected species diversity'. Unlike most parametric measures of diversity, the proposed index has a clear probabilistic interpretation, allowing at the same time a multiplicative partition of diversity into independent alpha and beta components for unequally weighted plots.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome 'La Sapienza', Piazzale Aldo Moro 5, Rome 00185, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1007/s12080-008-0028-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2009 - Computing parametric beta diversity with unequal plot weights A solution based on resampling methods.pdf:pdf},
-journal = {Theoretical Ecology},
-number = {1},
-pages = {13--17},
-title = {{Computing parametric beta diversity with unequal plot weights: A solution based on resampling methods}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-62349132351{\&}partnerID=40{\&}md5=19e3a0d1c6b833c4fc9799f31bd1d89d},
-volume = {2},
-year = {2009}
-}
-@book{MateuMahiques2009,
-address = {Oleiros, Spain},
-author = {{Mateu Mahiques}, Jorge and {Albert Ortiz}, Jos{\'{e}} Miguel and {Comas Rodr{\'{i}}guez}, Carles and {Orts R{\'{i}}os}, Vincente and {Pernias Cerrillo}, Jos{\'{e}} C and Porcu, Emilio},
-booktitle = {Series in Methodology and Data Analysis in Social Sciences},
-editor = {Mangin, Jean-Pierre L{\'{e}}vy},
-publisher = {Netbiblo},
-title = {{Stochastic Processes for Spatial Econometrics}},
-year = {2009}
-}
-@phdthesis{Guitet2015,
-author = {Guitet, St{\'{e}}phane},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guitet - 2015 - Diversit{\'{e}} des {\'{e}}cosyst{\`{e}}mes forestiers de Guyane fran{\c{c}}aise distribution, d{\'{e}}terminants et cons{\'{e}}quences en termes de servic.pdf:pdf},
-pages = {364},
-school = {Universit{\'{e}} de Montpellier},
-title = {{Diversit{\'{e}} des {\'{e}}cosyst{\`{e}}mes forestiers de Guyane fran{\c{c}}aise : distribution, d{\'{e}}terminants et cons{\'{e}}quences en termes de services {\'{e}}cosyst{\'{e}}miques}},
-type = {Th{\`{e}}se de Doctorat},
-year = {2015}
-}
-@article{Thompson1989,
-abstract = {The word coevolution has become a standard part of the lexicon of evolutionary biology. More than 1000 papers during the past decade have used coevolution in the title or abstract. Hundreds more have used the word in passing in the body of the paper. A half dozen books now include coevolution in the title. As usage of coevolution has increased, so have the views on the processes and mechanisms of coevolutionary change. The problem now is to understand the ecological and genetic conditions that favor different modes and outcomes of coevolution. {\textcopyright} 1989.},
-author = {Thompson, John N.},
-doi = {10.1016/0169-5347(89)90125-0},
-isbn = {0169-5347},
-issn = {01695347},
-journal = {Trends in Ecology and Evolution},
-number = {6},
-pages = {179--183},
-pmid = {21227347},
-title = {{Concepts of coevolution}},
-volume = {4},
-year = {1989}
-}
-@article{Dray2007,
-abstract = {Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number ofmultivariate methods. Its implementation follows the tradition of the French school of ”Analyse des Donn´ ees” and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy.},
-author = {Dray, St{\'{e}}phane and Dufour, Anne-B{\'{e}}atrice},
-doi = {10.18637/jss.v022.i04},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dray, Dufour - 2007 - The ade4 package implementing the duality diagram for ecologists.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {4},
-pages = {1--20},
-title = {{The ade4 package: implementing the duality diagram for ecologists}},
-url = {https://www.jstatsoft.org/article/view/v022i04},
-volume = {22},
-year = {2007}
-}
-@incollection{McFadden1974,
-address = {New York},
-author = {McFadden, Daniel},
-booktitle = {Frontiers in Econometrics},
-editor = {Zarembka, P},
-pages = {105--142},
-publisher = {Academic Press},
-title = {{Conditional Logit Analysis of Qualitative Choice Behavior}},
-year = {1974}
-}
-@article{Jaynes1957,
-abstract = {Information theory provides a constructive criterion for setting up probability distributions on the basis of partial knowledge, and leads to a type of statistical inference which is called the maximum-entropy estimate. it is the least biased estimate possible on the given information; i.e., it is maximally noncommital with regard to the missing information. If one considers statistical mechanics as a form of statistical inference rather than as a physical theory, it is found that the usual computational rules, starting with the determination of the partition function, are an immediate consequence of the maximum-entropy principle. In the resulting "subjective statistical mechanics", the usual rules are thus justified independently of any physical argument, and in particular independently of experimental verification; whether or not the results agree with experiment, they still represent the best estimates that cound have been made on the basis of the information available. It is concluded that statistical mechancis need not be regarded as a physical theory dependent for its validity on the truth of additional assumptions not contained in the laws of mechanics (such as ergodicity, metric transitivity, equal a priori probabilities, etc.). Furthermore, it is possible to maintain a sharp distinction between its physical and statistical aspects. The former consists only of the correct enumeration of the states of a system and their properties; the latter is a straightforward example of statistical inference.},
-author = {Jaynes, Edwin T.},
-doi = {10.1103/PhysRev.106.620},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaynes - 1957 - Information Theory and Statistical Mechanics.pdf:pdf},
-journal = {Physical Review},
-number = {4},
-pages = {1--11},
-title = {{Information Theory and Statistical Mechanics}},
-url = {https://journals.aps.org/pr/abstract/10.1103/PhysRev.106.620},
-volume = {106},
-year = {1957}
-}
-@article{Chytry2003,
-abstract = {In European phytosociology, variable plot sizes are traditionally used for sampling different vegetation types. This practice may generate problems in current vegetation or habitat survey projects based on large data sets, which include relev{\'{e}}s made by many authors at different times. In order to determine the extent of variation in plot sizes used in European phytosociology, we collected a data set of 41 174 relev{\'{e}}s with an indication of plot size, published in six major European journals focusing on phytosociology from 1970 to 2000. As an additional data set, we took 27 365 relev{\'{e}}s from the Czech National Phytosociological Database. From each data set, we calculated basic statistical figures for plot sizes used to sample vegetation of various phytosociological classes. The results show that in Europe the traditionally used size of vegetation plots is roughly proportional to vegetation height; however, there is a large variation in plot size, both within and among vegetation classes. The effect of variable plot sizes on vegetation analysis and classification is not sufficiently known, but use of standardized plot sizes would be desirable in future projects of vegetation or habitat survey. Based on our analysis, we suggest four plot sizes as possible standards. They are 4 m2 for sampling aquatic vegetation and low-grown herbaceous vegetation, 16 m2 for most grassland, heathland and other herbaceous or low-scrub vegetation types, 50 m2 for scrub, and 200 m2 for woodlands. It has been pointed out that in some situations, sampling in either small or large plots may result in assignment of relev{\'{e}}s to different phytosociological classes or habitat types. Therefore defining vegetation and habitat types as scale-dependent concepts is needed.},
-author = {Chytr{\'{y}}, Milan and Ot{\'{y}}pkov{\'{a}}, Zdenka},
-doi = {10.1111/j.1654-1103.2003.tb02183.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chytr{\'{y}}, Ot{\'{y}}pkov{\'{a}} - 2003 - Plot sizes used for phytosociological sampling of European vegetation.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {563--570},
-title = {{Plot sizes used for phytosociological sampling of European vegetation}},
-url = {http://dx.doi.org/10.1111/j.1654-1103.2003.tb02183.x},
-volume = {14},
-year = {2003}
-}
-@article{Llambi2004,
-abstract = {1 We analyse successional changes in local spatial structure of populations of a dominant late-successional species (Espeletia schultzii) in the high tropical Andes. 2 Spatial maps of plants of E. schultzii and important features of their environment were recorded at early (year 3) and middle (year 8) stages of succession after agricultural disturbance, and in non-cultivated paramo. 3 Spatial covariance functions were calculated from the maps to provide information on the changing 'plant-eye's view' of seedlings and adults during succession, and on the coupling of spatial structure to dynamics of successional communities. 4 Seedlings of E. schultzii appeared at high densities shortly after agricultural disturbance ceased. Spatial aggregation, which among seedlings was strongest in later stages of succession, was absent among adults, suggesting greater mortality within aggregations of conspecifics plays a part in regulating population dynamics. 5 Early in succession, seedlings of E. schultzii were slightly segregated from the dominant early successional species, Rumex acetosella. By year 8 of succession, R. acetosella was strongly segregated from adults of E. schultzii, but not from seedlings. This suggests that competitive exclusion caused by asymmetric competition may contribute to decline in early successional species. 6 Spatial sorting in relation to abiotic factors was most evident in the mature paramo, with E. schultzii adults occurring on steeper slopes and on less stony ground. E. schultzii adults here were also segregated from Hypericum laricifolium, the other dominant species. 7 The coupling of local spatial structure to community dynamics may have profound effects on succession. In particular, the development of interspecific segregation could contribute to the continued coexistence of early and late successional species throughout succession.},
-annote = {Article},
-author = {Llambi, Luis D. and Law, Richard and Hodge, Angela},
-doi = {10.1111/j.1365-2745.2004.00837.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Llambi, Law, Hodge - 2004 - Temporal changes in local spatial structure of late-successional species establishment of an Andean caulesce.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {122--131},
-title = {{Temporal changes in local spatial structure of late-successional species: establishment of an Andean caulescent rosette plant}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2004.00837.x/abstract},
-volume = {92},
-year = {2004}
-}
-@article{Coomes1999,
-abstract = {We describe a clump recognition process that may be used to analyze fully mapped spatial data. Any given spatial pattern can be made less aggregated by replacing the closest-together pair of plants by a single individual at their centroid position. By repeatedly amalgamating pairs of individuals in this way, an initially aggregated pattern can be reduced to one indistinguishable from complete spatial randomness (i.e. a two-dimensional Poisson pattern). The clump recognition process provides information on the size structure of aggregates within a population. Randomizing the position of clump centers can be used to generate patterns that have similar aggregation characteristic to the original pattern. This property is used to develop Monte Carlo simulations for testing interspecific associations. We also discuss tests of association that are based on measuring segregation between clump centers. We illustrate the methods with a series of patterns from (1) simple, stochastic processes, (2) a spatially explicit population model, and (3) a dune annual community.},
-annote = {Article
-English
-ECOLOGY
-174LK},
-author = {Coomes, David Anthony and Rees, Mark and Turnbull, Lindsay},
-doi = {10.1890/0012-9658(1999)080[0554:IAAAIF]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coomes, Rees, Turnbull - 1999 - Identifying aggregation and association in fully mapped spatial data.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {554--565},
-title = {{Identifying aggregation and association in fully mapped spatial data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(1999)080{\%}5B0554:IAAAIF{\%}5D2.0.CO{\%}3B2/full},
-volume = {80},
-year = {1999}
-}
-@article{Martinez2008,
-abstract = {The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. In any case, it is difficult to completely comprehend the global changes that occur in the transcriptome, given that thousands of gene expression measurements are involved. We propose an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. We define transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. We introduce the formulae using a simple example and show their application in two datasets of gene expression in human tissues. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. The framework presented enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli.},
-author = {Mart{\'{i}}nez, Octavio and Reyes-Vald{\'{e}}s, M. Humberto},
-doi = {10.1073/pnas.0803479105},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mart{\'{i}}nez, Reyes-Vald{\'{e}}s - 2008 - Defining diversity, specialization, and gene specificity in transcriptomes through information theory.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {28},
-pages = {9709--9714},
-title = {{Defining diversity, specialization, and gene specificity in transcriptomes through information theory}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/18606989},
-volume = {105},
-year = {2008}
-}
-@article{Blanco2015,
-abstract = {Shifting cultivation is the most widespread agroforestry system in the tropics that may contribute to biodiversity conservation under certain conditions. Despite their common use, traditional biodiversity indexes prove ill-suited for assessing complex systems of this type. This study proposes a novel index, AGB, to assess agrobiodiversity in systems that mix species, varieties, lifeforms, and uses. The AGB index was tested using agrobiodiversity inventories in Vanuatu, where we compared agrobiodiversity levels and patterns of change over the course of a crop cycle between different field types. The 297 sampled fields contained a total of 127 species with an average of 10.1 species and of 11.6 varieties per field. During the cropping cycle, species and varietal richness diminish. The AGB index was compared with the Shannon and Pielou indexes and proved to be accurate for assessing and monitoring agrobiodiversity at the species and varietal levels. It may be a useful tool for agrobiodiversity monitoring in agricultural systems undergoing changes in practices and for achieving a better understanding of their biocultural resilience.},
-author = {Blanco, Julien and Vandenbroucke, Henri and Carriere, St{\'{e}}phanie M.},
-doi = {10.1080/21683565.2015.1127307},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blanco, Vandenbroucke, Carriere - 2016 - A Novel Index to Quantify Agrobiodiversity in A Biocultural Perspective the Case of Shifting Cu.pdf:pdf},
-journal = {Agroecology and Sustainable Food Systems},
-number = {3},
-pages = {190--214},
-title = {{A Novel Index to Quantify Agrobiodiversity in A Biocultural Perspective: the Case of Shifting Cultivation Gardens in Vanuatu (Pacific)}},
-url = {http://www.tandfonline.com/doi/full/10.1080/21683565.2015.1127307},
-volume = {40},
-year = {2016}
-}
-@article{Grassberger2003,
-abstract = {We present a detailed derivation of some estimators of Shannon entropy for discrete distributions. They hold for finite samples of N points distributed into M "boxes", with N and M -{\textgreater} oo, but N/M {\textless} oo. In the high sampling regime ({\textless}{\textless} 1 points in each box) they have exponentially small biases. In the low sampling regime the errors increase but are still much smaller than for most other estimators. One advantage is that our main estimators are given analytically, with explicitly known analytical formulas for the biases.},
-author = {Grassberger, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grassberger - 2003 - Entropy Estimates from Insufficient Samplings.pdf:pdf},
-journal = {arXiv Physics e-prints},
-number = {v2},
-title = {{Entropy Estimates from Insufficient Samplings}},
-url = {http://arxiv.org/abs/physics/0307138},
-volume = {0307138},
-year = {2003}
-}
-@article{Lang2013,
-abstract = {Aggregation patterns are often visually detected in sets of location data. These clusters may be the result of interesting dynamics or the effect of pure randomness. We build an asymptotically Gaussian test for the hypothesis of randomness corresponding to a Poisson point process. We first compute the exact first and second moment of the Ripley K-statistic under the homogeneous Poisson point process model. Then we prove the asymptotic normality of a vector of such statistics for different scales and compute its covariance matrix. From these results, we derive a test statistic that is chi-square distributed. By a Monte-Carlo study, we check that the test is numerically tractable even for large data sets and also correct when only a hundred of points are observed.},
-archivePrefix = {arXiv},
-arxivId = {1006.1567},
-author = {Lang, Gabriel and Marcon, Eric},
-doi = {10.1051/ps/2012027},
-eprint = {1006.1567},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lang, Marcon - 2013 - Testing randomness of spatial point patterns with the Ripley statistic.pdf:pdf},
-journal = {ESAIM: Probability and Statistics},
-pages = {767--788},
-title = {{Testing randomness of spatial point patterns with the Ripley statistic}},
-url = {http://arxiv.org/abs/1006.1567},
-volume = {17},
-year = {2013}
-}
-@article{Soberon1993,
-abstract = {We develop a stochastic theory of the accumulation of new species in faunistic or floristic inventories. Differential equations for the expected list size and its variance as a function of the time spent collecting are presented and solved for particular cases. These particular cases correspond to different models of how the probability of adding a new species changes with time, the size of the list, the complexity of the area sampled, and other parameters. Examples using field data from butterflies and mammals are discussed, and it is argued that the equations relating sampling effort with size of the list may be useful for conservation purposes because they should lend formality to comparisons among lists and because they may have predictive power by extrapolating the asymptotic size of the lists. The suitability of different models to a variety of field situations is also discussed. Se presenta una teor{\'{i}}a estoc{\'{a}}stica de la acumulaci{\'{o}}n de especies nuevas en inventarios flor{\'{i}}sticos o faun{\'{i}}sticos. Se obtienen y resuelven casos particulares de las ecuaciones diferenciales que relacionan el tama{\~{n}}o esperado de las listas y su variancia con el tiempo dedicado a la colecta. Los casos particulares corresponden a diferentes modelos de c{\'{o}}mo la probabilidad de a{\~{n}}adir una especie nueva a la lista cambia con el tiempo, el tama{\~{n}}o de la lista, la complejidad del {\'{a}}rea y otros par{\'{a}}metros. Se discuten ejemplos con datos de campo de mariposas y mam{\'{i}}feros y se argumenta que el contar con ecuaciones que relacionen el esfuerzo de colecta con el tama{\~{n}}o del inventorio puede ser {\'{u}}til para prop{\'{o}}sitos conservacionistas porque se podr{\'{a}}n formalizar las comparaciones entre inventorios y porque tales ecuaciones pueden tener un valor predictivo al extrapolar para obtener los valores asint{\'{o}}ticos de las listas. Tambi{\'{e}}n se discute la conveniencia de los diferentes modelos a distintas situaciones de campo.},
-author = {{Sober{\'{o}}n M.}, Jorge and {Llorente B.}, Jorge},
-doi = {10.1046/j.1523-1739.1993.07030480.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sober{\'{o}}n M., Llorente B. - 1993 - The Use of Species Accumulation Functions for the Prediction of Species Richness.pdf:pdf},
-journal = {Conservation Biology},
-number = {3},
-pages = {480--488},
-title = {{The Use of Species Accumulation Functions for the Prediction of Species Richness}},
-url = {http://dx.doi.org/10.1046/j.1523-1739.1993.07030480.x},
-volume = {7},
-year = {1993}
-}
-@article{Wilson1968,
-abstract = {The analysis of caste ratios and their effect on colony efficiency can be approached by linear programming models. In the formulation offered here, account has been taken of certain general features of organization and behavior peculiar to insect societies; selection was assumed to be at the colony level; and the optimization goal was given as the maximum production of new queens and males by a mature colony whose size has an upper limit characteristic of the species. Even in their elementary form, the linear models here produced some interesting new conclusions, among which are the following: 1. Different kinds of contingencies, for which distinct behavioral responses are evolved (e.g., invasion by enemies, larval hunger, nest fouling), will be met by the colony as a whole in such a way that each kind of contingency causes about the same amount of reduction in average queen production. 2. Castes, including both physical variants and temporal behavioral stages, will tend to be proliferated in evolution until there is one and only one distinct caste specialized to meet each contingency. 3. The weight of workers belonging to a given caste at a given moment will increase in evolution according to the frequency and importance of the contingency to which it is specialized. 4. Under most, but not all, circumstances, it is of advantage to the colony progressively to increase the degree of specialization of each caste. 5. The more specialized the caste becomes, and in general the more efficient it becomes, the less will be its representation in the colony. This inverse relation between ability and numbers, which is a consequence of selection at the colony level, is the direct opposite of what would be predicted from selection at the level of the individual organism. 6. Proliferation of castes should be countered by those contingencies whose changes in frequency through time are poorly autocorrelated and paced so as to be difficult to track genetically. Certain changes in the environment can result in a caste being dropped, a result that at first seems paradoxical. This is due to the fact that, even though the caste is still the best one to handle a contingency that continues to be important, its presence nonetheless results in lowered efficiency of the colony as a whole. 7. The more specialized a caste has become, the less likely it is to be dropped from the optimal mix due to fluctuation in the environment. This, too, is the opposite of what would be expected if selection were operating at the level of the organism rather than at the colony level. 8. Certain empirically determined qualities of physical castes in ants and termites are consistent with the result of this ergonomic theory and, for the moment at least, seem best explained by it.},
-author = {Wilson, Edward O.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilson - 1968 - The ergonomics of caste in the social insects.pdf:pdf},
-journal = {American Naturalist},
-number = {6},
-pages = {25--35},
-title = {{The ergonomics of caste in the social insects}},
-url = {http://www.jstor.org/stable/2459048},
-volume = {68},
-year = {1968}
-}
-@article{Kuhn2004,
-author = {Kuhn, Ingolf and Durka, Walter and Klotz, Stefan},
-doi = {10.1111/j.1366-9516.2004.00106.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kuhn, Durka, Klotz - 2004 - BiolFlor - a new plant-trait database as a tool for plant invasion ecology.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {5-6},
-pages = {363--365},
-title = {{BiolFlor - a new plant-trait database as a tool for plant invasion ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1366-9516.2004.00106.x/abstract},
-volume = {10},
-year = {2004}
-}
-@article{Dufour-Kowalski2012,
-abstract = {Context Forest scientists build models to simulate stand growth and forests dynamics. Dedicated computer tools are often developed to implement these models in order to run silvicultural scenarios and explore simulation results. Aims Our objective was to encourage software reuse and simplify model implementation. Methods The scheme was to develop a framework and methodology allowing to simplify the implementation, integration, simulation and comparison of forest models by providing a set of common and standard tools. Results Capsis provides an open and modular software architecture based on various components, allowing to run forest growth simulations and display the results. The benefits of this framework are shown with the Samsara2 model, an individual-based and spatialised tree model. Capsis has been used successfully in many similar projects. In addition, the Capsis methodology defines how developers, modellers and end-users may interact. Conclusion The Capsis framework facilitates collaborative and shared software development. Moreover, it is a powerful way to support scientific animation in the frame of forest science.},
-author = {Dufour-Kowalski, Samuel and Courbaud, Beno{\^{i}}t and Dreyfus, Philippe and Meredieu, C{\'{e}}line and {De Coligny}, Fran{\c{c}}ois},
-doi = {10.1007/s13595-011-0140-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dufour-Kowalski et al. - 2012 - Capsis An open software framework and community for forest growth modelling.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {2},
-pages = {221--233},
-title = {{Capsis: An open software framework and community for forest growth modelling}},
-url = {https://link.springer.com/article/10.1007/s13595-011-0140-9},
-volume = {69},
-year = {2012}
-}
-@article{Knevel2003,
-abstract = {An international group of scientists is building a 'trait base', an open internet database of life-history traits of the Northwest European flora (LEDA) that can be used as a tool in planning, in nature conservation and restoration, and in other applied research. The species-trait matrix will comprise referenced information under control of an editorial board, for species of the Northwest European flora, combining existing information and additional measurements. The focus will be on 26 plant traits that describe three key features of plant dynamics: persistence. regeneration, and dispersability. Currently 35{\%} of the species-trait matrix has been filled; however. as the LEDA trait base consortium aims to deliver a database as complete as possible, all input from the scientific community is welcome.},
-author = {Knevel, I. C. and Bekker, Ren{\'{e}}e M. and Bakker, J. P. and Kleyer, M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Knevel et al. - 2003 - Life-history traits of the northwest European flora The LEDA database.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {611--614},
-title = {{Life-history traits of the northwest European flora: The LEDA database}},
-volume = {14},
-year = {2003}
-}
-@article{Sarkar2014,
-abstract = {The goal of this work is to describe some connections between cryptology and statistics. Starting from basic frequency analysis, throughout history, statistical ideas have been employed to attack cryptographic systems and continue to be important in modern day cryptanalysis. Brief descriptions of hypothesis testing based distinguishing attacks, differential cryptanalysis and statistical ideas used in side channel attacks are provided. From the designer's point of view, we consider three connections. A brief description is provided of the cryptographic ideas that have been suggested to strengthen the technique of randomised response. In recent times, a new notion of privacy of statistical databases has arisen and has been called differential privacy. We provide a brief description of this idea and mention some of its applications. Lastly, we consider the problem of defining and proving security of public key encryption schemes and provide a simple example of this method. It is hoped that the topics outlined here will motivate researchers to further investigate the connection between these two subjects.},
-author = {Sarkar, Palash},
-doi = {10.1016/j.jspi.2013.05.008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sarkar - 2014 - On some connections between statistics and cryptology.pdf:pdf},
-journal = {Journal of Statistical Planning and Inference},
-pages = {20--37},
-title = {{On some connections between statistics and cryptology}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0378375813001110},
-volume = {148},
-year = {2014}
-}
-@article{Courchamp2014,
-abstract = {Fundamental ecology is the basis for understanding our complex biological world. •Funding for fundamental research over the past few decades has been at lower levels than that for other major research categories. •We provide several ways forward to promote fundamental research in the future. •Promoting fundamental ecology is a multi-actor problem involving scientists, research institutions, funding bodies, and politicians.},
-author = {Courchamp, Franck and Dunne, Jennifer A. and {Le Maho}, Yvon and May, Robert M. and Th{\'{e}}baud, Christophe and Hochberg, Michael E.},
-doi = {10.1016/j.tree.2014.11.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Courchamp et al. - 2014 - Fundamental ecology is fundamental.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {1},
-pages = {9--16},
-title = {{Fundamental ecology is fundamental}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534714002444},
-volume = {30},
-year = {2015}
-}
-@article{Rocchini2013,
-abstract = {The assessment of species diversity in relatively large areas has always been a challenging task for ecologists, mainly because of the intrinsic difficulty to judge the completeness of species lists and to undertake sufficient and appropriate sampling. Since the variability of remotely sensed signal is expected to be related to landscape diversity, it could be used as a good proxy of diversity at species level.It has been demonstrated that the relation between species and landscape diversity measured from remotely sensed data or land use maps varies with scale. However, Free and Open Source tools (allowing an access to the source code) for assessing landscape diversity at different spatial scales are still lacking today. In this paper, we aim at: i) providing a theoretical background of the mostly used diversity indices stemmed from information theory that are commonly applied to quantify landscape diversity from remotely sensed data and ii) proposing a free and robust Open Source tool (r.diversity) with its source code for calculating diversity indices (and allowing an easy potential implementation of new metrics by multiple contributors globally) at different spatial scales from remotely-sensed imagery or land use maps, running under the widely used Open Source program GRASS GIS.r.diversity can be a valuable tool for calculating landscape diversity in an Open Source space given the availability of multiple indices at multiple spatial scales with the possibility to create new indices directly reusing the code.We expect that the subject of this paper will stimulate discussions on the opportunities offered by Free and Open Source Software to calculate landscape diversity indices. {\textcopyright} 2012 Elsevier B.V.},
-annote = {Cited By (since 1996):2
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Rocchini, D.; Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, GIS and Remote Sensing Unit, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy; email: duccio.rocchini@fmach.it},
-author = {Rocchini, Duccio and Delucchi, Luca and Bacaro, Giovanni and Cavallini, Paolo and Feilhauer, Hannes and Foody, Giles M. and He, Kate S. and Nagendra, Harini and Porta, Claudio and Ricotta, Carlo and Schmidtlein, Sebastian and Spano, Lucio Davide and Wegmann, Martin and Neteler, Markus},
-doi = {10.1016/j.ecoinf.2012.04.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rocchini et al. - 2013 - Calculating landscape diversity with information-theory based indices A GRASS GIS solution(2).pdf:pdf},
-journal = {Ecological Informatics},
-pages = {82--93},
-title = {{Calculating landscape diversity with information-theory based indices: A GRASS GIS solution}},
-url = {http://www.sciencedirect.com/science/article/pii/S1574954112000295},
-volume = {17},
-year = {2013}
-}
-@article{Pastor1998,
-abstract = {The effects of herbivores on landscape patterns and ecosystem processes have generally been inferred only from small-plot or exclosure experiments. However, it is important to directly determine the interactions between herbivores and landscape patterns, because herbivores range over large portions of the landscape to meet requirements for food and shelter. In two valleys on Isle Royale, Michigan, USA, soil nitrogen availability and its temporal variance decreased rapidly as consumption of browse by moose (Alces alces) increased up to 2 g.m-2.yr-1; with greater amounts of consumption, nitrogen availability was uniformly low and constant from year to year. We tested three geostatistical models of the spatial distribution of available browse, annual browse consumption, conifer basal area, and soil nitrogen availability across the landscape: (1) no spatial autocorrelation (random spatial distribution); (2) short-range spatial autocorrelation within a patch, but random distribution of patches at larger scales (spherical model); and (3) both short-range autocorrelation within a patch and regular arrangement of patches at larger scales (harmonic oscillator model). Conifer basal area and soil nitrogen availability fit the harmonic oscillator model in both valleys. Annual consumption and available browse showed oscillations in one of the valleys and only short-range autocorrelation in the other. In both valleys, however, the spatial pattern of annual consumption followed that of available browse. The predominance of spatially oscillatory patterns suggests that the interactions of moose with the forest ecosystem cause the development of both local patches of vegetation and associated nitrogen cycling rates, as well as the development of higher order patterns across the larger landscape. We suggest a coupled diffusion model of herbivore foraging and plant seed dispersal that may account for these patterns.},
-author = {Pastor, John and Dewey, Bradley and Moen, Ronald and Mladenoff, David J. and White, Mark and Cohen, Yosef},
-doi = {10.1890/1051-0761(1998)008[0411:SPITMF]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pastor et al. - 1998 - Spatial Patterns in the Moose-Forest-Soil Ecosystem on Isle Royale, Michigan, USA.pdf:pdf},
-journal = {Ecological Applications},
-number = {2},
-pages = {411--424},
-title = {{Spatial Patterns in the Moose-Forest-Soil Ecosystem on Isle Royale, Michigan, USA}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/1051-0761(1998)008{\%}5B0411:SPITMF{\%}5D2.0.CO;2/abstract},
-volume = {8},
-year = {1998}
-}
-@article{Poorter2006,
-abstract = {Tree architecture is an important determinant of the height extension, light capture, and mechanical stability of trees, and it allows species to exploit the vertical height gradient in the forest canopy and horizontal light gradients at the forest floor. Tropical tree species partition these gradients through variation in adult stature (H-max) and light demand. In this Study we compare 22 architectural traits for 54 Bolivian moist-forest tree species. We evaluate how architectural traits related to H-max vary with tree size, and we present a conceptual scheme in which we combine the two axes into four different functional groups. Interspecific correlations between architecture and H a, varied strongly from negative to positive, depending on the reference sizes used. Stem height was positively related to H-max at larger reference diameters (14-80 cm). Species height vs. diameter curves often flattened toward their upper ends in association with reproductive maturity for species of all sizes. Thus, adult understory trees were typically shorter than similar-diameter juveniles of larger species. Crown area was negatively correlated with H-max at small reference heights and positively correlated at larger reference heights (15-34 m). Wide crowns allow the small understory species to intercept light over a large area at the expense of a reduced height growth. Crown length was negatively correlated with H-max at intermediate reference heights (4-14 m). A long crown enables small understory species to maximize light interception in a light-limited environment. Light-demanding species were characterized by orthotropic stems and branches, large leaves, and a monolayer leaf arrangement. They realized an efficient height growth through the formation of narrow and shallow crowns. Light demand turned out to be a much stronger predictor of tree architecture than Hmax, probably because of the relatively low, open, and semi-evergreen canopy at the research site. The existence of four functional groups (shade-tolerant, partial-shade-tolerant, and long- and short-lived pioneer) was confirmed by the principal component and discriminant analysis: Both light demand and H-max capture the major variation in functional traits found among tropical rain forest tree species, and the two-way classification scheme provides a straightforward model to understand niche differentiation in tropical forests.},
-author = {Poorter, Lourens and Bongers, Laurent and Bongers, Frans},
-doi = {10.1890/0012-9658(2006)87[1289:AOMTST]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Poorter, Bongers, Bongers - 2006 - Architecture of 54 moist-forest tree species Traits, trade-offs, and functional groups.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1289--1301},
-title = {{Architecture of 54 moist-forest tree species: Traits, trade-offs, and functional groups}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2006)87[1289:AOMTST]2.0.CO;2/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Bajo2002,
-abstract = {In this paper we provide a connection between concentration and inequality by showing that the inequality measures consistent with the whole class of Hannah-Kay concentration indices are the general entropy inequality indices. We isolate the inequality component underlying the concentration measures, obtaining and explicit additive decomposition of the change in concentration into the change in its two components: inequality and the number of firms. This relationship proves to be valid for the whole class of Hannah-Kay concentration indices, and embodies as particular cases other previously found in the literature. Finally, our proposed decomposition is shown by means of an empirical example, which ilustrates the sources of a change in sectoral concentration between two points in time.},
-author = {Bajo, Oscar and Salas, Rafael},
-doi = {10.1007/s101080200053},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bajo, Salas - 2002 - Inequality foundations of concentration measures An application to the Hannah-Kay indices.pdf:pdf},
-journal = {Spanish Economic Review},
-number = {4},
-pages = {311--316},
-title = {{Inequality foundations of concentration measures: An application to the Hannah-Kay indices}},
-url = {http://dx.doi.org/10.1007/s101080200053},
-volume = {4},
-year = {2002}
-}
-@article{Takahashi2005,
-abstract = {Leaf nitrogen content per area (N-area) is a good indicator of assimilative capacity of leaves of deciduous broad-leaved trees. This study examined the degrees of increase in Narea in response to canopy openings as leaf mass per area (LMA) and leaf nitrogen content per mass (N-mass) in saplings of eight deciduous broad-leaved tree species in Hokkaido, northern Japan. Five of the species were well-branched species with a large number of small leaves (lateral-growth type), and the other three species were less-branched species with a small number of large leaves (vertical-growth type). The degrees of increase in Narea were compared between the two crown types. In closed-canopy conditions, leaves of the vertical-growth species tended to have a lower LMA and higher N-mass than those of the lateral-growth species, which resulted in similar N-area for both. LMA increased in canopy openings in the eight species, and the degrees of increase were not largely different between the lateral- and vertical-growth species. On the contrary, N-mass was unchanged in canopy openings in the eight species. As a result, N-area of each species increased in canopy openings in proportion to the increase in LMA, and the degrees of increase in N-area were similar in the lateral- and vertical-growth species. Therefore, this study showed that the degrees of increase in N-area were not correlated with the crown architecture (i.e., the lateral- and vertical-growth types).},
-author = {Takahashi, Kochi and Seino, Tatsuyuki and Kohyama, Takashi},
-doi = {10.1007/s11284-004-0003-z},
-file = {::},
-journal = {Ecological Research},
-number = {1},
-pages = {17--23},
-title = {{Plastic changes of leaf mass per area and leaf nitrogen content in response to canopy openings in saplings of eight deciduous broad-leaved tree species}},
-url = {https://link.springer.com/article/10.1007/s11284-004-0003-z},
-volume = {20},
-year = {2005}
-}
-@article{Goulard1995,
-abstract = {The relationship between the locations of the clumps of sprouts, some morphological characteristics of the clumps and the local soil environment in an old sweet chestnut coppice are studied. The theory of marked point process, which has not yet been used extensively in forestry studies, is shown to be adequate for the analysis of this type of spatial data. The marks correspond to morphological characteristics of the clumps: “diameter”, “number of sprouts”, “height at one year”, and “height at three years”. Several covariance functions are described which give a method for exploring the spatial relationships within the stand. Some of these functions are introduced for the first time in an actual statistical analysis. By using these functions, it is shown that the clumps are regularly distributed. The variables “diameter” and “number of sprouts” are strongly spatially negatively correlated, whereas the heights are slightly or not correlated. By categorising the individuals according to the mark values, it is shown that the small clumps tended to be aggregated in the gaps between medium and large clumps. Values of heights in the ties of the distribution are related as well as their spatial correlation to the local soil environment.},
-author = {Goulard, M. and Pages, L. and Cabanettes, A.},
-doi = {10.1002/bimj.4710370707},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Goulard, Pages, Cabanettes - 1995 - Marked point process using correlation functions to explore a spatial data set.pdf:pdf},
-journal = {Biometrical Journal},
-number = {7},
-pages = {837--853},
-title = {{Marked point process: using correlation functions to explore a spatial data set}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/bimj.4710370707/abstract},
-volume = {37},
-year = {1995}
-}
-@article{Ceballos2017,
-abstract = {The population extinction pulse we describe here shows, from a quantitative viewpoint, that Earth's sixth mass extinction is more severe than perceived when looking exclusively at species extinc-tions. Therefore, humanity needs to address anthropogenic popula-tion extirpation and decimation immediately. That conclusion is based on analyses of the numbers and degrees of range contraction (indicative of population shrinkage and/or population extinctions according to the International Union for Conservation of Nature) using a sample of 27,600 vertebrate species, and on a more detailed analysis documenting the population extinctions between 1900 and 2015 in 177 mammal species. We find that the rate of population loss in terrestrial vertebrates is extremely high—even in " species of low concern. " In our sample, comprising nearly half of known vertebrate species, 32{\%} (8,851/27,600) are decreasing; that is, they have de-creased in population size and range. In the 177 mammals for which we have detailed data, all have lost 30{\%} or more of their geographic ranges and more than 40{\%} of the species have experienced severe population declines ({\textgreater}80{\%} range shrinkage). Our data indicate that beyond global species extinctions Earth is experiencing a huge epi-sode of population declines and extirpations, which will have nega-tive cascading consequences on ecosystem functioning and services vital to sustaining civilization. We describe this as a " biological an-nihilation " to highlight the current magnitude of Earth's ongoing sixth major extinction event. sixth mass extinction | population declines | population extinctions | conservation | ecosystem service},
-author = {Ceballos, Gerardo and Ehrlich, Paul R. and Dirzo, Rodolfo},
-doi = {10.1073/pnas.1704949114},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ceballos, Ehrlich, Dirzo - 2017 - Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses.pdf:pdf},
-issn = {0027-8424},
-journal = {Proceedings of the National Academy of Sciences},
-pages = {201704949},
-title = {{Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines}},
-url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1704949114},
-year = {2017}
-}
-@article{Baraloto2010c,
-abstract = {We examined fine-scale heterogeneity of environmental conditions in a primary rain forest in French Guiana to describe variation in microhabitats that plants may experience during establishment. We characterized both the range as well as the spatial structuring of 11 environmental factors important for seedling establishment in six hexagonal sampling grids, one each in gap and understory sites at three points representing the predominant geomorphic units in this primary forest. Each grid contained 37 sampling points separated by 31 cm-20 m. Monte-Carlo tests of semivariograms against complete spatial randomness indicated that for many variables in all six sampling grids, spatial dependence did not exceed 1 m. A principal component analysis of all sampling points revealed a lack of spatial microhabitat structure, rather than homogeneous patches associated with canopy structure or geomorphology. Our results suggest that ample fine-scale spatial heterogeneity exists to support the coexistence of plant species with differential abiotic requirements for regeneration.},
-author = {Baraloto, Christopher and Couteron, Pierre},
-doi = {10.1111/j.1744-7429.2009.00620.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto, Couteron - 2010 - Fine-scale microhabitat heterogeneity in a french guianan forest.pdf:pdf},
-journal = {Biotropica},
-number = {4},
-pages = {420--428},
-title = {{Fine-scale microhabitat heterogeneity in a french guianan forest}},
-volume = {42},
-year = {2010}
-}
-@article{Muscarella2016,
-abstract = {The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of 173 tree species in Puerto Rico. We tested the hypothesis that species are more likely to occur where their trait values are more similar to the local CWM trait values (the'CWM-optimality' hypothesis) by comparing species occurrence patterns (as a proxy for fitness) with the functional composition of forest plots across a precipitation gradient. While 70{\%} of the species supported CWM-optimality for at least one trait, nearly 25{\%} significantly opposed it for at least one trait, thereby contributing to local functional diversity. The majority (85{\%}) of species that opposed CWM-optimality did so only for one trait and few species opposed CWM-optimality in multivariate trait space. Our study suggests that constraints to local functional variation act more strongly on multivariate phenotypes than on univariate traits.},
-author = {Muscarella, Robert and Uriarte, Mar{\'{i}}a},
-doi = {10.1098/rspb.2015.2434},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Muscarella, Uriarte - 2016 - Do community-weighted mean functional traits reflect optimal strategies.pdf:pdf},
-isbn = {0962-8452$\backslash$r1471-2954},
-issn = {0962-8452},
-journal = {Proceedings of the Royal Society B: Biological Sciences},
-number = {1827},
-pages = {20152434},
-title = {{Do community-weighted mean functional traits reflect optimal strategies?}},
-url = {http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2015.2434},
-volume = {283},
-year = {2016}
-}
-@article{Dumay2004,
-abstract = {Ten functional traits of fish species were related to habitat, diet or food acquisition, to propose a classification of 21 lagoon fishes into 10 functional groups. The selection of traits was based on their functional interest and the ease of measurement. Some groups were taxonomically related containing species belonging to the same genus, e.g. Syngnathus, Atherina or Pomatochistus. Species with a flat body shape constituted another group and three species (Anguilla anguilla, Gambusia affinis and Callionymus pusillus) formed individual groups. These results could be used to constitute functional units and to simplify such complex ecosystems and their interactions.},
-annote = {Article},
-author = {Dumay, Olivier and Tari, P. S. and Tomasini, Jean-Antoine and Mouillot, David},
-doi = {10.1111/j.1095-8649.2004.00365.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dumay et al. - 2004 - Functional groups of lagoon fish species in Languedoc Roussillon, southern France.pdf:pdf},
-journal = {Journal of Fish Biology},
-number = {4},
-pages = {970--983},
-title = {{Functional groups of lagoon fish species in Languedoc Roussillon, southern France}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8649.2004.00365.x/full},
-volume = {64},
-year = {2004}
-}
-@article{Runkle1989,
-author = {Runkle, James R.},
-doi = {10.2307/1940199},
-issn = {00129658},
-journal = {Ecology},
-month = {jun},
-number = {3},
-pages = {546--547},
-title = {{Synchrony of Regeneration, Gaps, and Latitudinal Differences in Tree Species Diversity}},
-url = {http://doi.wiley.com/10.2307/1940199},
-volume = {70},
-year = {1989}
-}
-@article{Garnier1997,
-abstract = {The study of the relationship between species richness of a plant community and its productivity has received much attention, recently renewed by the concern on the loss of biological diversity at a global scale. Here, we briefly review some indices widely used in agronomic and competition experiments to compare monocultures and mixtures, and compare them to other, more recently designed ones. These various indices are then calculated for two experiments. In the first experiment, two grass and two legume species were grown at six levels of nitrogen availability, either in monocultures or in mixtures of the four species in a substitutive design; in the second experiment, five grass species were grown at 16 levels of total nutrient availability, either in monocultures or in mixtures of the five species in an additive design. These data clearly show that the conclusions drawn from the experiments depend on the index used to compare the experimental communities. We argue that a clear test of whether the productivity of communities increases with species richness requires that: (1) all species present in the multispecies assemblages also be grown in monocultures under the same environmental conditions, and (2) the productivity of these assemblages be compared to the most productive monoculture. We conclude that there are as yet very few cases where superior productivity of multispecies assemblages as compared to monocultures has been clearly shown.},
-author = {Garnier, Eric and Navas, Marie-Laure and Austin, Michael P. and Lilley, Julianne M. and Gifford, Roger M.},
-doi = {10.1016/S1146-609X(97)80049-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garnier et al. - 1997 - A problem for biodiversity-productivity studies how to compare the productivity of multispecific plant mixtures.pdf:pdf},
-journal = {Acta Oecologica},
-number = {6},
-pages = {657--670},
-title = {{A problem for biodiversity-productivity studies: how to compare the productivity of multispecific plant mixtures to that of monocultures?}},
-url = {http://www.sciencedirect.com/science/article/pii/S1146609X97800495},
-volume = {18},
-year = {1997}
-}
-@article{Glaeser1992,
-abstract = {Recent theories of economic growth, including those of Romer, Porter, and Jacobs, have stressed the role of technological spillovers in generating growth. Because such knowledge spillovers are particularly effective in cities, where communication between people is more extensive, data on the growth of industries in different cities allow us to test some of these theories. Using a new data set on the growth of large industries in 170 U.S. cities between 1956 and 1987, we find that local competition and urban variety, but not regional specialization, encourage employment growth in industries. The evidence suggests that important knowledge spillovers might occur between rather than within industries, consistent with the theories of Jacobs.},
-author = {Glaeser, Edward L. and Kallal, Heidi D. and Scheinkman, Jos{\'{e}} A. and Schleifer, Andrei},
-doi = {10.1086/261856},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Glaeser et al. - 1992 - Growth in Cities.pdf:pdf},
-journal = {Journal of Political Economy},
-number = {6},
-pages = {1126--1152},
-title = {{Growth in Cities}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/261856},
-volume = {100},
-year = {1992}
-}
-@incollection{Chao2004,
-address = {New York},
-author = {Chao, Anne},
-booktitle = {Encyclopedia of Statistical Sciences},
-edition = {2nd ed.},
-editor = {Balakrishnan, N and Read, C B and Vidakovic, B},
-publisher = {Wiley},
-title = {{Species richness estimation}},
-year = {2004}
-}
-@article{Barot1999a,
-abstract = {A comprehensive analysis was conducted of the spatial pattern of a Borassus aethiopum population and its environment, to infer links between demographic processes, plant spatial patterns and environmental heterogeneity. B. aethiopum has easily identifiable demographic stages, a root foraging strategy enabling adults to reach distant nutrient sources, and a marked senescence starting with the onset of reproduction. Map data was analysed for palm individuals (in 3 different life history stages plus 2 sexes for adults) and for nutrient-rich patches (clumps of other tree species and termite mounds) in 3 vegetation types in humid savanna in West Africa (Lamto, Ivory Coast). Spatial analyses were based on Diggle's nearest neighbour functions F and G and on Ripley's K function. Juveniles and seedlings were aggregated, while adults had a random pattern or were more loosely aggregated. All stages except female adults were spatially associated with nutrient- rich patches, but association distances increased with stage in the life cycle, and seedlings were associated with female adults, whereas the association of juveniles at longer distances was not clear-cut. It is suggested that a parsimonious scenario exists linking spatial pattern and mortality pattern during the life cycle. The initial pattern of seedlings (close to maternal trees) resulted from low dispersal distance, while later stages (older seedlings and juveniles) were mostly restricted to nutrient-rich patches through nutrient shortage away from these patches (environment-induced mortality) and form dense clumps of immature palms. Competition on nutrient-rich patches then favoured the few juveniles that manage to survive farther from these patches (density-dependent mortality). The last surviving juvenile of a clump suddenly experiences almost no competition with conspecifics, due to the long distance between clumps of juveniles, and owing to its root-foraging ability, it can now recruit to the adult stage, subject only to senescence.},
-author = {Barot, S{\'{e}}bastien and Gignoux, Jacques and Menaut, Jean-Claude.},
-doi = {10.1890/0012-9658(1999)080[1987:DOASPT]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barot, Gignoux, Menaut - 1999 - Demography of a savanna palm tree predictions from comprehensive spatial pattern analyses(2).pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1987--2005},
-title = {{Demography of a savanna palm tree: predictions from comprehensive spatial pattern analyses}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(1999)080{\%}5B1987:DOASPT{\%}5D2.0.CO{\%}3B2/abstract},
-volume = {80},
-year = {1999}
-}
-@article{Goreaud2003,
-abstract = {The interactions between plants of different species, age or size play an important role in the dynamics of an ecosystem and can induce specific structures. These interactions can be studied by analysing the spatial structure of the corresponding bivariate patterns. The intertype L12-function has recently been successfully used in many papers for that purpose. However, when interpreting the results obtained with ecological data, at least two different null hypotheses – independence or random labelling – can be appropriate, depending on the context of the study and the nature of the data. As these two hypotheses correspond to different confidence intervals, an inappropriate choice of the null hypothesis can lead to misinterpretations of biotic interactions when studying ecological data. This problem has rarely been mentioned in the literature. In this paper we clarify the differences between these two null hypotheses, and illustrate the risk of misinterpretation when using an inappropriate null hypothesis. We review the main characteristics of these two hypotheses, and analyse the spatial structure of both real data from forest stands and simulated virtual stands of different structures. We demonstrate that the risk of misinterpretation is quite high, and that extreme misinterpretations, i.e. cases leading to opposite conclusions in terms of spatial interaction, can occur in a significant number of cases. We therefore propose some guidelines to help ecologists avoid such misinterpretations.},
-author = {Goreaud, Fran{\c{c}}ois and P{\'{e}}lissier, Rapha{\"{e}}l},
-doi = {10.1111/j.1654-1103.2003.tb02200.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Goreaud, P{\'{e}}lissier - 2003 - Avoiding misinterpretation of biotic interactions with the intertype K12 function population independence vs.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {681--692},
-title = {{Avoiding misinterpretation of biotic interactions with the intertype K12 function: population independence vs random labelling hypotheses}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2003.tb02200.x/abstract},
-volume = {14},
-year = {2003}
-}
-@article{Lopez-Martinez2013,
-abstract = {Two main theories have attempted to explain variation in plant species composition ($\beta$-diversity). Niche theory proposes that most of the variation is related to environment (environmental filtering), whereas neutral theory posits that dispersal limitation is the main driver of $\beta$-diversity. In this study, we first explored how $\alpha$- and $\beta$-diversity of plant functional groups defined by growth form (trees, shrubs and lianas, which represent different strategies of resource partitioning), and dispersal syndrome (autochory, anemochory and zoochory, which represent differences in dispersal limitation) vary with successional age and topographic position in a tropical dry forest. Second, we examined the effects of environmental, spatial, and spatially-structured environmental factors on $\beta$-diversity of functional groups; we used the spatial structure of sampling sites as a proxy for dispersal limitation, and elevation, soil properties and forest stand age as indicators of environmental filtering. We recorded 200 species and 22,245 individuals in 276 plots; 120 species were trees, 41 shrubs and 39 lianas. We found that $\beta$-diversity was highest for shrubs, intermediate for lianas and lowest for trees, and was slightly higher for zoochorous than for autochorous and anemochorous species. All three dispersal syndromes, trees and shrubs varied in composition among vegetation classes (successional age and topographic position), whilst lianas did not. $\beta$-diversity was influenced mostly by proxies of environmental filtering, except for shrubs, for which the influence of dispersal limitation was more important. Stand age and topography significantly influenced $\alpha$-diversity across functional groups, but showed a low influence on $\beta$-diversity –possibly due to the counterbalancing effect of resprouting on plant distribution and composition. Our results show that considering different plant functional groups reveals important differences in both $\alpha$- and $\beta$-diversity patterns and correlates that are not apparent when focusing on overall woody plant diversity, and that have important implications for ecological theory and biodiversity conservation.},
-author = {L{\'{o}}pez-Mart{\'{i}}nez, Jorge Omar and Sanaphre-Villanueva, Luc{\'{i}}a and Dupuy, Juan Manuel and Hern{\'{a}}ndez-Stefanoni, Jos{\'{e}} Luis and Meave, Jorge Arturo and Gallardo-Cruz, Jos{\'{e}} Alberto},
-doi = {10.1371/journal.pone.0073660},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/L{\'{o}}pez-Mart{\'{i}}nez et al. - 2013 - $\beta$-Diversity of Functional Groups of Woody Plants in a Tropical Dry Forest in Yucatan.pdf:pdf},
-journal = {Plos One},
-number = {9},
-pages = {e73660},
-title = {{$\beta$-Diversity of Functional Groups of Woody Plants in a Tropical Dry Forest in Yucatan}},
-url = {http://dx.doi.org/10.1371{\%}2Fjournal.pone.0073660},
-volume = {8},
-year = {2013}
-}
-@book{Stevens1996,
-abstract = {This book combines an introduction to the major theoretical concepts in general ecology with the programming language R, a cutting edge Open Source tool. Starting with geometric growth and proceeding through stability of multispecies interactions and species-abundance distributions, this book demystifies and explains fundamental ideas in population and community ecology. Graduate students in ecology, along with upper division undergraduates and faculty, will all find this to be a useful overview of important topics.},
-author = {Stevens, Martin Henry Hoffman},
-doi = {10.1007/978-0-387-89882-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stevens - 1996 - A Primer of Ecology with R.pdf:pdf},
-isbn = {978-0-387-89881-0},
-number = {6},
-pages = {265},
-publisher = {Springer},
-title = {{A Primer of Ecology with R}},
-volume = {11},
-year = {1996}
-}
-@article{Chave2003,
-abstract = {We review various aspects of the notion of scale applied to natural systems, in particular complex adaptive systems. We argue that scaling issues are not only crucial from the standpoint of basic science, but also in many applied issues, and discuss tools for detecting and dealing with multiple scales, both spatial and temporal. We also suggest that the techniques of statistical mechanics, which have been successful in describing many emergent patterns in physical systems, can also prove useful in the study of complex adaptive systems.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Levin, Simon},
-doi = {10.1023/B:EARE.0000007348.42742.49},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Levin - 2003 - Scale and scaling in ecological and economic systems.pdf:pdf},
-journal = {Environmental {\&} Resource Economics},
-number = {4},
-pages = {527--557},
-title = {{Scale and scaling in ecological and economic systems}},
-url = {https://link.springer.com/article/10.1023/B:EARE.0000007348.42742.49},
-volume = {26},
-year = {2003}
-}
-@article{Augustine2003,
-abstract = {Despite increasing recognition of the role spatial pattern can play in ecosystem function, few studies have quantified spatial heterogeneity in savanna ecosystems. The spatial distribution of herbaceous biomass and species composition was measured across three scales in a semi-arid savanna in central Kenya, and patterns were related to environmental variables at different scales. Herbaceous biomass declined across a rainfall gradient and from upper to lower topographic positions, but variation within a site (across 5-50 m) was similar in magnitude to among-site variation associated with rainfall and topography. Geostatistical analyses showed that patchiness at scales of 5-25 m explained 20{\%} of total variation in herbaceous biomass. This pattern arose from the presence of both 5-10-m diameter patches containing high herbaceous biomass ({\textgreater}170 g m(-2)) and 5-10-m diameter patches characterized by nearly bare soil surfaces ({\textless}40 g m(-2)). Patch structure was contingent on topography, with larger bare patches at ridgeline and upper hillslope positions. Grass species distributions showed the greatest degree of patch structure and species turnover across distances of 5-45 m. Additional community variation was associated with topography, with minimal variation in species composition across the rainfall gradient. Pattern diversity significantly exceeded levels reported for four other grassland ecosystems, suggesting fundamental differences in local processes generating spatial pattern. It is hypothesized that heterogeneously distributed grazing pressure, interacting with the distribution of shrub canopies, is an important factor generating such high levels of small-scale patch structure in this savanna.},
-annote = {Article
-English
-PLANT ECOL
-684KC},
-author = {Augustine, David J.},
-doi = {10.1023/A:1023927512590},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Augustine - 2003 - Spatial heterogeneity in the herbaceous layer of a semi-arid savanna ecosystem.pdf:pdf},
-journal = {Plant Ecology},
-number = {2},
-pages = {319--332},
-title = {{Spatial heterogeneity in the herbaceous layer of a semi-arid savanna ecosystem}},
-url = {http://link.springer.com/article/10.1023/A:1023927512590},
-volume = {167},
-year = {2003}
-}
-@article{Beck2009,
-abstract = {The formalism of statistical mechanics can be generalised by starting from more general measures of information than the Shannon entropy and maximising those subject to suitable constraints. We discuss some of the most important examples of information measures that are useful for the description of complex systems. Examples treated are the R{\'{e}}nyi entropy, Tsallis entropy, Abe entropy, Kaniadakis entropy, Sharma?Mittal entropies, and a few more. Important concepts such as the axiomatic foundations, composability and Lesche stability of information measures are briefly discussed. Potential applications in physics include complex systems with long-range interactions and metastable states, scattering processes in particle physics, hydrodynamic turbulence, defect turbulence, optical lattices, and quite generally driven nonequilibrium systems with fluctuations of temperature.},
-author = {Beck, Christian},
-doi = {10.1080/00107510902823517},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beck - 2009 - Generalised Information and Entropy Measures in Physics.pdf:pdf},
-journal = {Contemporary Physics},
-number = {4},
-pages = {495--510},
-title = {{Generalised Information and Entropy Measures in Physics}},
-url = {http://dx.doi.org/10.1080/00107510902823517},
-volume = {50},
-year = {2009}
-}
-@article{Bacaro2012a,
-abstract = {Similarity in species composition among different areas plays an essential task in biodiversity management and conservation since it allows the identification of those environmental gradients that functionally operate in determining vari- ation in species composition across spatial scale. The decay of compositional similarity with increasing spatial or environmental distance derives from: 1) the presence of spatial constraints which create a physical separation among habitats, or 2) the decrease in environmental similarity with increasing distance. Even if the distance decay of compositional similarity represents a well known pattern characterising all types of biological communities, few attempts were made to examine this pattern at small spatial scales with respect to both grain and extent. Aim of this work was to test whether the distance decay of similarity 1) can be observed at a local scale in situations where environmental conditions are relatively homogeneous and ecological barriers are absent, and 2) is dependent on the grain size at which plant community data are recorded. We selected two urban brownfields located at Bremen university campus, Germany, of 40 m ? 20 m each, systematically divided in nested plots with an increasing spatial scale of 0.25 m2, 1 m2, 4 m2 and 16 m2. Both plant species composition and soil variables were recorded in each cell. Linear and logarithmic least squares regression models were applied in order to examine the decay of similarity due to spatial distance (calculated as the Euclidean distance among pairs of plots) and environmental distance (calculated as the Euclidean distance among PCA-transformed soil variables). A general lack of distance decay was observed, irrespective of the type of distance (spatial or environmental) or the grain size. We argue that this is probably due to a random variation both of the important environmental parameters and of the local distribution patterns of individual species, the latter mainly caused by the high dispersal abilities of the majority of species occurring in the brownfields.},
-author = {Bacaro, Giovanni and Rocchini, D. and Dupr{\`{e}}, C. and Diekmann, M. and Carnesecchi, F. and Gori, V. and Chiarucci, A.},
-doi = {10.1556/ComEc.13.2012.1.5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro et al. - 2012 - Absence of distance decay in the similarity of plots at small extent in an urban brownfield.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {36--44},
-title = {{Absence of distance decay in the similarity of plots at small extent in an urban brownfield}},
-url = {http://www.akademiai.com/openurl.asp?genre=article{\&}id=doi:10.1556/ComEc.13.2012.1.5},
-volume = {13},
-year = {2012}
-}
-@article{Gorelick2006,
-abstract = {Shannon's and Simpson's indices have been the most widely accepted measures of ecological diversity for the past fifty years, even though neither statistic accounts for species abundances across geographic locales (‘‘patches''). An abundant species that is endemic to a single patch can be as much of a conservation concern as a rare cosmopolitan species. I extend Shannon's and Simpson's indices to simultaneously account for species richness and relative abundances ? i.e. extend them to multispecies metacommunities ? by making the inputs to each index a matrix, rather than a vector. The Shannon's index analogue of diversity is mutual entropy of species and patches divided by marginal entropy of the individual geographic patches. The Simpson's index analogue of diversity is a modification of mutual entropy, with the logarithm moved to the outside of the summation, divided by Simpson's index of the patches. Both indices are normalized for number of patches, with the result being inversely proportional to biodiversity. These methods can be extended to account for time-series of such matrices and average age-classes of each species within each patch, as well as provide a measure of spatial coherence of communities. R.},
-author = {Gorelick, Root},
-doi = {10.1111/j.0906-7590.2006.04601.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gorelick - 2006 - Combining richness and abundance into a single diversity index using matrix analogues of Shannon's and Simpson's indic.pdf:pdf},
-journal = {Ecography},
-number = {4},
-pages = {525--530},
-title = {{Combining richness and abundance into a single diversity index using matrix analogues of Shannon's and Simpson's indices}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2006.04601.x/abstract},
-volume = {29},
-year = {2006}
-}
-@article{Legendre2015,
-abstract = {* The Mantel test is widely used in biology, including landscape ecology and genetics, to detect spatial structures in data or control for spatial correlation in the relationship between two data sets, for example community composition and environment. The study demonstrates that this is an incorrect use of that test. * The null hypothesis of the Mantel test differs from that of correlation analysis; the statistics computed in the two types of analyses differ. We examined the basic assumptions of the Mantel test in spatial analysis and showed that they are not verified in most studies. We showed the consequences, in terms of power, of the mismatch between these assumptions and the Mantel testing procedure. * The Mantel test H0 is the absence of relationship between values in two dissimilarity matrices, not the independence between two random variables or data tables. The Mantel R2 differs from the R2 of correlation, regression and canonical analysis; these two statistics cannot be reduced to one another. Using simulated data, we show that in spatial analysis, the assumptions of linearity and homoscedasticity of the Mantel test (H1: small values of D1 correspond to small values of D2 and large values of D1 to large values of D2) do not hold in most cases, except when spatial correlation extends over the whole study area. Using extensive simulations of spatially correlated data involving different representations of geographic relationships, we show that the power of the Mantel test is always lower than that of distance-based Moran's eigenvector map (dbMEM) analysis and that the Mantel R2 is always smaller than in dbMEM analysis, and uninterpretable. These simulation results are novel contributions to the Mantel debate. We also show that regression on a geographic distance matrix does not remove the spatial structure from response data and does not produce spatially uncorrelated residuals. * Our main conclusion is that Mantel tests should be restricted to questions that, in the domain of application, only concern dissimilarity matrices, and are not derived from questions that can be formulated as the analysis of the vectors and matrices from which one can compute dissimilarity matrices.},
-author = {Legendre, Pierre and Fortin, Marie-Jos{\'{e}}e and Borcard, Daniel},
-doi = {10.1111/2041-210X.12425},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Fortin, Borcard - 2015 - Should the Mantel test be used in spatial analysis.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {11},
-pages = {1239--1247},
-title = {{Should the Mantel test be used in spatial analysis?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12425/abstract},
-volume = {6},
-year = {2015}
-}
-@article{Shimatani2001,
-abstract = {Multivariate point processes were applied to introducing two functions indicating spatial variation of species diversity when mapped data are given. They are extensions of the Simpson index of species diversity. The one function, alpha (r), is defined as the probability that a randomly selected pair of individuals within distance r belong to different species. The other function, beta (r), is the conditional probability that the two individuals belong to different species given that their distance is r. The functions were applied to examining the effects of thinning favoring desirable species in mixed hardwood forest on multispecies spatial patterns and biodiversity. Low alpha (r) and beta (r) for small r and high beta (r) for intermediate r in the thinned plots mean that the thinning involved forming single-species dominant patches. In contrast, almost constant alpha (r) and alpha (r) show that every species is uniformly distributed over the unthinned plots. However, if the largest 50{\%} trees in DBH were selected, the thinned plots have higher diversity at the almost all distances and higher overall diversity. (C) 2001 Elsevier Science B.V. All rights reserved.},
-annote = {Shimatani, K},
-author = {Shimatani, Kenichiro},
-doi = {10.1016/s0378-1127(00)00352-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shimatani - 2001 - Multivariate point processes and spatial variation of species diversity.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {215--229},
-title = {{Multivariate point processes and spatial variation of species diversity}},
-volume = {142},
-year = {2001}
-}
-@article{Dufrene1997,
-abstract = {This paper presents a new and simple method to find indicator species and species assemblages characterizing groups of sites. The novelty of our approach lies in the way we combine a species relative abundance with its relative frequency of occurrence in the various groups of sites. This index is maximum when all individuals of a species are found in a single group of sites and when the species occurs in all sites of that group; it is a symmetric indicator. The statistical significance of the species indicator values is evaluated using a randomization procedure. Contrary to TwrNSPAN, our indicator index for a given species is independent of the other species relative abundances, and there is no need to use pseudospecies. The new method identifies indicator species for typologies of species releves obtained by any hierarchical or nonhierarchical classification procedure; its use is independent of the classification method. Because indicator species give ecological meaning to groups of sites, this method provides criteria to compare typologies, to identify where to stop dividing clusters into subsets, and to point out the main levels in a hierarchical classification of sites. Species can be grouped on the basis of their indicator values for each clustering level, the heterogeneous nature of species assemblages observed in any one site being well pre- served. Such assemblages are usually a mixture of eurytopic (higher level) and stenotopic species (characteristic of lower level clusters). The species assemblage approach demon- strates the importance of the "sampled patch size," i.e., the diversity of sampled ecological combinations, when we compare the frequencies of core and satellite species. A new way to present species-site tables, accounting for the hierarchical relationships among species, is proposed. A large data set of carabid beetle distributions in open habitats of Belgium is used as a case study to illustrate the new method.},
-author = {Dufr{\^{e}}ne, Marc and Legendre, Pierre},
-doi = {10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dufr{\^{e}}ne, Legendre - 1997 - Species assemblages and indicator species the need for a flexible asymmetrical approach.pdf:pdf},
-journal = {Ecological monographs},
-number = {3},
-pages = {345--366},
-title = {{Species assemblages and indicator species: the need for a flexible asymmetrical approach}},
-url = {http://www.esajournals.org/doi/abs/10.1890/0012-9615(1997)067{\%}5B0345:SAAIST{\%}5D2.0.CO;2},
-volume = {67},
-year = {1997}
-}
-@article{Reardon2002,
-abstract = {In this paper we derive and evaluate measures of multigroup segregation. After describing four ways to conceptualize the measurement of multigroup segregation-as the disproportionality in group (e.g., race) proportions across organizational units (e.g., schools or census tracts), as the strength of association between nominal variables indexing group and organizational unit membership, as the ratio of between-unit diversity to total diversity and as the weighted average of two-group segregation indices-we derive six multigroup segregation indices: a dissimilarity index (D), a Gini index (G), an information theory index (H), a squared coefficient of variation index (C), a relative diversity index (R), and a normalized exposure index (P), We evaluate these six indices against a set of seven desirable properties of segregation indices. We conclude that the information theory index H is the most conceptually and mathematically satisfactory index, since it alone obeys the principle of transfers in the multigroup case. Moreover, H is the only multigroup index that can be decomposed into a sum of between- and within-group components.},
-annote = {ISI Document Delivery No.: BV13U
-Times Cited: 74
-Cited Reference Count: 45
-Reardon, SF Firebaugh, G
-BLACKWELL PUBL},
-author = {Reardon, S. F. and Firebaugh, G.},
-doi = {10.1111/1467-9531.00110},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reardon, Firebaugh - 2002 - Measures of multigroup segregation.pdf:pdf},
-journal = {Sociological Methodology},
-pages = {33--67},
-title = {{Measures of multigroup segregation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9531.00110/abstract},
-volume = {32},
-year = {2002}
-}
-@article{Scherer-Lorenzen2003,
-abstract = {The relationship between plant diversity and nitrate leaching into groundwater was investigated in a mid-European semi-natural grassland ecosystem. An experimental approach was used to directly manipulate plant diversity in the field, while holding other environmental factors constant. Species loss was simulated by establishing grassland communities of 16, 8, 4, 2, 1, and 0 plant species, composed of 3, 2, or I functional groups (grasses. legumes, and non-legume herbs). Every diversity treatment was replicated with several different species mixtures. Nitrate leaching was determined by continuous extraction of soil solution below the rooting zone and modeling of seepage rates. The concentration of nitrate in the soil solution was highly variable within each level of diversity. In bare ground plots and several low-diversity mixtures containing legumes, nitrate concentrations were higher than the official European Union threshold value for drinking water of 50 mg/L, with maximum values of up to 350 mg/L measured in Trifolium pratense monocultures. Total annual loss of nitrate was unaffected by the number of plant species or functional groups, but it was highly dependent on the specific species composition of the communities, and plots with legumes lost significantly more nitrate than plots without them. Aboveground biomass had no influence on nitrate loss, whereas leaching was negatively correlated with increasing root biomass. The abundance of legumes within a community, litter decomposition rates, and net nitrification were all positively correlated with total nitrate loss. However, in those communities containing legumes, leaching decreased with increasing diversity, because higher species richness led to a reduction in legume dominance, to a reduced nitrate supply through nitrification, and to a complementary uptake of nitrate by grasses and non-leguminous herbs. Based on these results, we expect that increasing the diversity of non-leguminous species or functional groups would reduce the risk of nitrate leaching in low-diversity grass-clover mixtures of ley-farming systems, while allowing for a more efficient exploitation of the beneficial fertilization effect provided by legumes.},
-author = {Scherer-Lorenzen, M. and Palmborg, C. and Prinz, A. and Schulze, E. D.},
-doi = {10.1890/0012-9658(2003)084[1539:TROPDA]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scherer-Lorenzen et al. - 2003 - The role of plant diversity and composition for nitrate leaching in grasslands.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1539--1552},
-title = {{The role of plant diversity and composition for nitrate leaching in grasslands}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282003{\%}29084[1539:TROPDA]2.0.CO{\%}3B2/abstract},
-volume = {84},
-year = {2003}
-}
-@article{North1998,
-abstract = {Truffles are a staple food source for many forest small mammals, yet the vegetation or soil conditions associated with truffle abundance are unknown. The spatial distribution of forest structures, organic layer depth, root density, and two of the most common western North American truffles (Elaphomyces granulatus and Rhizopogon parksii) were examined in managed- young, natural-mature and old-growth western hemlock (Tsuga heterophylla)/Douglas fir (Pseudotsuga menziesii) stands in Washington State, USA. Forest conditions and E. granulatus and R. parksii sporocarp locations were mapped and analysed using ARC/INFO. Spatial patterns were assessed with univariate and bivariate Ripley's K analysis, which measures the scale at which one and two sets of points, respectively, are 'attracted' or 'repelled'. R. parksii truffles were not associated with organic layer depth, root density or forest structure. E. granulatus truffles were distributed in widely-spaced, high- biomass clusters which are significantly associated with thick organic layers with a high density of fine roots. E. granulatus truffles were significantly distanced from trees at 1-2 m. No other associations were found between E. granulatus truffles, logs, ferns or shrubs. Although E. granulatus comprised more than 90{\%} of the total truffle biomass in the unmanaged mature and old-growth stands, in managed-young stands, E. granulatus truffles were rare and total truffle biomass was low. In managed-young stands, organic layer depth and fine root density have been significantly reduced by the introduction of fire. Slash burning and soil scarification practices in these forests may have a strong affect on local food abundance and availability of the most common truffle for small mammal consumers.},
-author = {North, Malcolm and Greenberg, Joshua},
-doi = {10.1016/S0378-1127(98)00310-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/North, Greenberg - 1998 - Stand conditions associated with truffle abundance in western hemlockDouglas-fir forests.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1/2},
-pages = {55--66},
-title = {{Stand conditions associated with truffle abundance in western hemlock/Douglas-fir forests}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112798003107},
-volume = {112},
-year = {1998}
-}
-@article{Mouquet2012,
-abstract = {Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.},
-author = {Mouquet, Nicolas and Devictor, Vincent and Meynard, Christine N. and Munoz, Fran{\c{c}}ois and Bersier, Louis-F{\'{e}}lix and Chave, J{\'{e}}r{\^{o}}me and Couteron, Pierre and Dalecky, Ambroise and Fontaine, Colin and Gravel, Dominique and Hardy, Olivier J. and Jabot, Franck and Lavergne, S{\'{e}}bastien and Leibold, Mathew and Mouillot, David and M{\"{u}}nkem{\"{u}}ller, Tamara and Pavoine, Sandrine and Prinzing, Andreas and Rodrigues, Ana S. L. and Rohr, Rudolf P. and Th{\'{e}}bault, Elisa and Thuiller, Wilfried},
-doi = {10.1111/j.1469-185X.2012.00224.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouquet et al. - 2012 - Ecophylogenetics advances and perspectives.pdf:pdf},
-journal = {Biological Reviews},
-number = {4},
-pages = {769--785},
-title = {{Ecophylogenetics: advances and perspectives}},
-url = {http://dx.doi.org/10.1111/j.1469-185X.2012.00224.x},
-volume = {87},
-year = {2012}
-}
-@article{Stoyan1985,
-author = {Stoyan, Dietrich and Ohser, J},
-doi = {10.1137/1129043},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan, Ohser - 1985 - Cross-Correlation Measures of Weighted Random Measures and Their Estimation.pdf:pdf},
-journal = {Theory of Probability and its Applications},
-number = {2},
-pages = {345--355},
-title = {{Cross-Correlation Measures of Weighted Random Measures and Their Estimation}},
-url = {http://epubs.siam.org/doi/abs/10.1137/1129043},
-volume = {29},
-year = {1985}
-}
-@phdthesis{Goreaud2000a,
-address = {Nancy},
-author = {Goreaud, Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Goreaud - 2000 - Apports de l'analyse de la structure spatiale en for{\^{e}}t temp{\'{e}}r{\'{e}}e {\`{a}} l'{\'{e}}tude de la mod{\'{e}}lisation des peuplements complexes.pdf:pdf},
-school = {ENGREF},
-title = {{Apports de l'analyse de la structure spatiale en for{\^{e}}t temp{\'{e}}r{\'{e}}e {\`{a}} l'{\'{e}}tude de la mod{\'{e}}lisation des peuplements complexes}},
-year = {2000}
-}
-@article{Swenson2012,
-author = {Swenson, Nathan G. and Erickson, David L. and Mi, Xiangcheng and Bourg, Norman A. and Forero-Monta{\~{n}}a, Jimena and Ge, Xuejun and Howe, Robert and Lake, Jeffrey K. and Liu, Xiaojuan and Ma, Keping and Pei, Nancai and Thompson, Jill and Uriarte, Mar{\'{i}}a and Wolf, Amy and Wright, S. Joseph and Ye, Wanhui and Zhang, Jinlong and Zimmerman, Jess K. and Kress, W. John},
-doi = {10.1890/11-0402.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Swenson et al. - 2012 - Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities.pdf:pdf},
-isbn = {0012-9658},
-journal = {Ecology},
-number = {sp8},
-pages = {S112--S125},
-publisher = {Ecological Society of America},
-title = {{Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities}},
-url = {http://dx.doi.org/10.1890/11-0402.1},
-volume = {93},
-year = {2012}
-}
-@article{Villeger2017,
-abstract = {Sobral et al. (Ecology Letters, 19, 2016, 1091) reported that the loss of bird functional and phylogenetic diversity due to species extinctions was not compensated by exotic species introductions. Here, we demonstrate that the reported changes in biodiversity were underestimated because of methodological pitfalls.},
-author = {Vill{\'{e}}ger, S{\'{e}}bastien and Maire, Eva and Leprieur, Fabien},
-doi = {10.1111/ele.12750},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vill{\'{e}}ger, Maire, Leprieur - 2017 - On the risks of using dendrograms to measure functional diversity and multidimensional spaces t(2016).pdf:pdf},
-journal = {Ecology Letters},
-title = {{On the risks of using dendrograms to measure functional diversity and multidimensional spaces to measure phylogenetic diversity: a comment on Sobral et al . (2016)}},
-url = {http://doi.wiley.com/10.1111/ele.12750},
-volume = {in press},
-year = {2017}
-}
-@techreport{Aiginger1999,
-author = {Aiginger, Karl},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Aiginger - 1999 - Do industrial structures converge A survey on the empirical literature on specialization and concentration of industri.pdf:pdf},
-keywords = {Aiginger (1999).pdf},
-mendeley-tags = {Aiginger (1999).pdf},
-title = {{Do industrial structures converge? A survey on the empirical literature on specialization and concentration of industries}},
-year = {1999}
-}
-@article{Perez-Harguindeguy2013,
-abstract = {In this paper, we have reviewed how the hydraulic design of trees influences the movement of water from roots to leaves. The hydraulic architecture of trees can limit their water relations, gas exchange throughout the crown of trees, the distribution of trees over different habitats and, perhaps, even the maximum height that a particular species can achieve. Parameters of particular importance include: (1) the vulnerability of stems to drought-induced cavitation events because cavitation reduces the hydraulic conductance of stems, (2) the leaf specific conductivity of stems because it determines the pressure gradients and most negative water potentials needed to sustain evaporation from leaves, (3) the water storage capacity of tissues because this might determine the ability of trees to survive long drought periods. All of these parameters are determined by the structure and function of anatomical components of trees. Some of the ecological and physiological trade-offs of specific structures are discussed.},
-author = {P{\'{e}}rez-Harguindeguy, N. and D{\'{i}}az, Sandra and Garnier, Eric and Lavorel, Sandra and Poorter, Hendrik and Jaureguiberry, P. and Bret-Harte, M. Syndonia and Cornwell, W. K. and Craine, J. M. and Gurvich, D. E. and Urcelay, C. and Veneklaas, E. J. and Reich, Peter B. and Poorter, Lourens and Wright, Ian J. and Ray, P. and Enrico, L. and Pausas, J. G. and {De Vos}, A. C. and Buchmann, N. and Funes, G. and Qu{\'{e}}tier, F and Hodgson, J. G. and Thompson, Ken and Morgan, H. D. and ter Steege, Hans and van der Heijden, M. G. A. and Sack, L. and Blonder, Benjamin and Poschlod, P. and Vaieretti, M. V. and Conti, G. and Staver, A. C. and Aquino, S. and Cornelissen, J. Hans C.},
-doi = {10.1071/BT12225},
-file = {::},
-journal = {Australian Journal of Botany},
-number = {3},
-pages = {715--716},
-title = {{New handbook for standardised measurement of plant functional traits worldwide}},
-url = {http://www.publish.csiro.au/bt/BT12225},
-volume = {61},
-year = {2013}
-}
-@misc{Mahfoud2007,
-address = {Aalborg University, Denmark},
-author = {Mahfoud, Ilene and Josselin, Didier and Fady, Bruno},
-booktitle = {10th AGILE International Conference on Geographic Information Science},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mahfoud, Josselin, Fady - 2007 - Effect of the aggregation process on the diversity assessment toward the 'pertinent scale'.pdf:pdf},
-title = {{Effect of the aggregation process on the diversity assessment: toward the 'pertinent scale'}},
-year = {2007}
-}
-@article{Stoyan1992,
-abstract = {The paper gives formulae for various distributional characteristics of planar Neyman-Scott processes. Some of them can be used for statistical estimation of model parameters.},
-author = {Stoyan, Dietrich},
-doi = {10.1007/BF02613983},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan - 1992 - Statistical estimation of model parameters of planar Neyman-Scott cluster processes.pdf:pdf},
-journal = {Metrika},
-pages = {67--74},
-title = {{Statistical estimation of model parameters of planar Neyman-Scott cluster processes}},
-url = {http://link.springer.com/article/10.1007{\%}2FBF02613983},
-volume = {39},
-year = {1992}
-}
-@article{Fernandez-Gonzalez2005,
-abstract = {Spatial events largely determine the biology of cells, tissues, and organs. In this paper, we present a tool for the quantitative spatial analysis of heterogeneous cell populations, and we show experimental validation of this tool using both artificial and real (mammary gland tissue) data, in two and three dimensions. We present the refined relative neighborhood graph as a means to establish neighborhood between cells in an image while modeling the topology of the tissue. Then, we introduce the M function as a method to quantitatively evaluate the existence of spatial patterns within one cell population or the relationship between the spatial distributions of multiple cell populations. Finally, we show a number of examples that demonstrate the feasibility of our approach.},
-author = {Fernandez-Gonzalez, Rodrigo and Barcellos-Hoff, Mary Helen and de Solorzano, Carlos Ortiz},
-doi = {10.1109/TIP.2005.852466},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fernandez-Gonzalez, Barcellos-Hoff, de Solorzano - 2005 - A Tool for the Quantitative Spatial Analysis of Complex Cellular Systems.pdf:pdf},
-journal = {IEEE Transactions on Image Processing},
-number = {9},
-pages = {1300--1313},
-title = {{A Tool for the Quantitative Spatial Analysis of Complex Cellular Systems}},
-url = {http://ieeexplore.ieee.org/document/1495503/},
-volume = {14},
-year = {2005}
-}
-@article{Carlton1983,
-author = {Carlton, Denis W},
-doi = {10.2307/1924189},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carlton - 1983 - The Location and Employment Choices of New Firms An Econometric Model With Discrete and Continuous Endogenous Variables.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {3},
-pages = {440--449},
-title = {{The Location and Employment Choices of New Firms: An Econometric Model With Discrete and Continuous Endogenous Variables}},
-url = {http://www.jstor.org/stable/1924189},
-volume = {65},
-year = {1983}
-}
-@article{Baraloto2010b,
-abstract = {• The elucidation of relationships between biodiversity and ecosystem processes has been limited by the definition of metrics of biodiversity and their integration into experimental design. Functional trait screening can strengthen the performance of these designs. • We suggest the use of Rao's quadratic entropy to measure both functional diversity and phyloge- netic diversity of species mixtures proposed for an experimental design, and demonstrate how they can provide complementary information. • We also present an index assessing the statistical performance of these independent variables in different experimental designs. Measurement of independent variables as continuous vs. discrete variables reduces statistical performance, but improves the model by quantifying species differences masked by group assignments. • To illustrate these advances, we present an example from a tropical forest tree community in which we screened 38 species for nine functional traits. The proposed TropiDEP design is based on the relative orthogonality of two multivariate trait axes defined using principal component analysis. • We propose that independent variables describing functional diversitymight be grouped to calculate independent variables describing suites of different traits with potentially different effects on partic- ular ecosystem processes. In other systems these axes may differ from those reported here, yet the methods of analysis integrating functional and phylogenetic diversity into experimental design could be universal.},
-author = {Baraloto, Christopher and Marcon, Eric and Morneau, Fran{\c{c}}ois and Pavoine, Sandrine and Roggy, Jean-Christophe},
-doi = {10.1051/forest/2009110},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2010 - Integrating functional diversity into tropical forest plantation designs to study ecosystem processes.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {3},
-pages = {303},
-title = {{Integrating functional diversity into tropical forest plantation designs to study ecosystem processes}},
-url = {http://link.springer.com/article/10.1051{\%}2Fforest{\%}2F2009110},
-volume = {67},
-year = {2010}
-}
-@misc{Connell1971,
-abstract = {Connell, J. H. 1971. On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. Pp. 298-312 in P. J. den Boer and G. R. Gradwell, eds., Dynamics of Populations. Centre for Agricultural Publishing and Documentation, Wageningen, The Netherlands.},
-author = {Connell, J. H.},
-booktitle = {Dynamics of populations},
-doi = {10.1890/07-2056.1},
-isbn = {978-9022003558},
-pages = {298--312},
-title = {{On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees}},
-url = {http://scholar.google.de/scholar?hl=de{\&}q=On+the+role+of+natural+enemies+in+preventing+competitive+exclusion+in+some+marine+animals+and+in+rain+forest+trees{\&}btnG={\&}lr={\#}0},
-volume = {298},
-year = {1971}
-}
-@article{Box1964,
-abstract = {In the analysis of data it is often assumed that observations y,, y,, ...,y, are independently normally distributed with constant variance and with expectations specified by a model linear in a set of parameters 0. In this paper we make the less restrictive assumption that such a normal, homo- scedastic, linear model is appropriate after some suitable transformation has been applied to the y's. Inferences about the transformation and about the parameters of the linear model are made by computing the likelihood function and the relevant posterior distribution. The contributions of normality, homoscedasticity and additivity to the transformation are separated. The relation of the present methods to earlier procedures for finding transformations is discussed. The methods are illustrated with examples.},
-author = {Box, G. E. P. and Cox, D. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Box, Cox - 1964 - An analysis of transformations Applying the Box-Cox transformation.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {211--252},
-title = {{An analysis of transformations}},
-url = {http://www.jstor.org/stable/2984418},
-volume = {26},
-year = {1964}
-}
-@article{Burnham1978,
-author = {Burnham, K. P. and Overton, W. S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Burnham, Overton - 1978 - Estimation of the Size of a Closed Population when Capture Probabilities vary Among Animals.pdf:pdf},
-journal = {Biometrika},
-number = {3},
-pages = {625--633},
-title = {{Estimation of the Size of a Closed Population when Capture Probabilities vary Among Animals}},
-volume = {65},
-year = {1978}
-}
-@incollection{Runnegar1987,
-address = {London},
-author = {Runnegar, B.},
-booktitle = {Rates of Evolution},
-editor = {Campbell, M. and Day, M. F.},
-pages = {39--60},
-publisher = {Allen {\&} Unwin},
-title = {{Rates and Modes of Evolution in the Mollusca}},
-year = {1987}
-}
-@article{Cadotte2010,
-abstract = {Phylogenetic information is increasingly being used to understand the assembly of biological communities and ecological processes. However, commonly used metrics of phylogenetic diversity (PD) do not incorporate information on the relative abundances of individuals within a community. In this study, we develop three indices of PD that explicitly consider species abundances. First, we present a metric of phylogenetic-abundance evenness that evaluates the relationship between the abundance and the distribution of terminal branch lengths. Second, we calculate an index of hierarchical imbalance of abundances at the clade level encapsulating the distribution of individuals across the nodes in the phylogeny. Third, we develop an index of abundance-weighted evolutionary distinctiveness and generate an entropic index of phylogenetic diversity that captures both information on evolutionary distances and phylogenetic tree topology, and also serves as a basis to evaluate species conservation value. These metrics offer measures of phylogenetic diversity incorporating different community attributes. We compare these new metrics to existing ones, and use them to explore diversity patterns in a typical California annual grassland plant community at the Jasper Ridge biological preserve. Ecology Letters (2010) 13: 96-105.},
-annote = {Cadotte, Marc W. Davies, T. Jonathan Regetz, James Kembel, Steven W. Cleland, Elsa Oakley, Todd H.},
-author = {Cadotte, Marc W. and Davies, T. J. and Regetz, J. and Kembel, S. W. and Cleland, E. and Oakley, T. H.},
-doi = {10.1111/j.1461-0248.2009.01405.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte et al. - 2010 - Phylogenetic diversity metrics for ecological communities integrating species richness, abundance and evolutiona.pdf:pdf},
-journal = {Ecology Letters},
-number = {1},
-pages = {96--105},
-title = {{Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01405.x/abstract},
-volume = {13},
-year = {2010}
-}
-@article{Dengler2009,
-abstract = {Aim The aims of this study are to resolve terminological confusion around different types of species–area relationships (SARs) and their delimitation from species sampling relationships (SSRs), to provide a comprehensive overview of models and analytical methods for SARs, to evaluate these theoretically and empirically, and to suggest a more consistent approach for the treatment of species–area data.Location Curonian Spit in north-west Russia and archipelagos world-wide.Methods First, I review various typologies for SARs and SSRs as well as mathematical models, fitting procedures and goodness-of-fit measures applied to SARs. This results in a list of 23 function types, which are applicable both for untransformed (S) and for log-transformed (log S) species richness. Then, example data sets for nested plots in continuous vegetation (n = 14) and islands (n = 6) are fitted to a selection of 12 function types (linear, power, logarithmic, saturation, sigmoid) both for S and for log S. The suitability of these models is assessed with Akaike's information criterion for S and log S, and with a newly proposed metric that addresses extrapolation capability.Results SARs, which provide species numbers for different areas and have no upper asymptote, must be distinguished from SSRs, which approach the species richness of one single area asymptotically. Among SARs, nested plots in continuous ecosystems, non-nested plots in continuous ecosystems, and isolates can be distinguished. For the SARs of the empirical data sets, the normal and quadratic power functions as well as two of the sigmoid functions (Lomolino, cumulative beta-P) generally performed well. The normal power function (fitted for S) was particularly suitable for predicting richness values over ten-fold increases in area. Linear, logarithmic, convex saturation and logistic functions generally were inappropriate. However, the two sigmoid models produced unstable results with arbitrary parameter estimates, and the quadratic power function resulted in decreasing richness values for large areas.Main conclusions Based on theoretical considerations and empirical results, I suggest that the power law should be used to describe and compare any type of SAR while at the same time testing whether the exponent z changes with spatial scale. In addition, one should be aware that power-law parameters are significantly influenced by methodology.},
-author = {Dengler, J{\"{u}}rgen},
-doi = {10.1111/j.1365-2699.2008.02038.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dengler - 2009 - Which function describes the species-area relationship best A review and empirical evaluation.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {4},
-pages = {728--744},
-title = {{Which function describes the species-area relationship best? A review and empirical evaluation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2008.02038.x/abstract},
-volume = {36},
-year = {2009}
-}
-@article{Zink2004,
-abstract = {It is generally assumed that the Quaternary was a period of heightened diversification in temperate vertebrate organisms. Previous molecular systematics studies have challenged this assertion. We re-examined this issue in north temperate birds using log-lineage plots and distributions of sister-taxon distances. Log-lineage plots support earlier conclusions that avian diversification slowed during the Quaternary. To test plots of empirical sister-taxon distances we simulated three sets of phylogenies: constant speciation and extinction, a pulse of recent speciation, and a pulse of recent extinction. Previous opinions favour the model of recent speciation although our empirical dataset on 74 avian comparisons failed to reject a distribution derived from the constant and extinction models. Hence, it does not appear that the Quaternary was a period of exceptional rates of diversification, relative to the background rate.},
-author = {Zink, R. M. and Klicka, J. and Barber, B. R.},
-doi = {10.1098/rstb.2003.1392},
-isbn = {0962-8436},
-issn = {0962-8436},
-journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
-number = {1442},
-pages = {215--220},
-pmid = {15101578},
-title = {{The tempo of avian diversification during the Quaternary}},
-url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2003.1392},
-volume = {359},
-year = {2004}
-}
-@article{DeJong1975,
-abstract = {Species diversity was calculated using three different indices on sets of real and artificial data. Each index was analyzed to determine its relationship to the two component parts of diversity, richness and evenness. Shannon's information formula, H{\^{a}}€²= C{\^{I}}{\pounds} p i log2 p i, is found to be linearly related to evenness and to the log2 of the number of species. Simpson's Index, D=1-{\^{a}}ˆ‘ n( n-1)/ N( N-1) and McIntosh's Index, {\$}{\{}\backslashrm D{\}}{\^{}}{\{}\backslashprime{\}}={\{}\backslashtextstyle\backslashfrac{\{}{\{}\backslashrm N{\}}-\backslashsurd \backslashoverline{\{}\backslashSigma {\{}\backslashrm n{\}}{\_}{\{}{\{}\backslashrm i{\}}{\}}{\{}{\}}{\^{}}{\{}2{\}}{\}}{\}}{\{}{\{}\backslashrm N{\}}-\backslashsurd \backslashoverline{\{}{\{}\backslashrm N{\}}{\}}{\}}{\}}{\$}, when expressed in probits are found to be linearly related to evenness and to the log2 of the number of species. Relationships between, and usefulness of, the indices are discussed. /// Ра{\~{N}} {\~{N}} {\~{N}}‡Ð¸{\~{N}}‚ено видовое {\~{N}}€Ð°Ð{\textperiodcentered}нооб{\~{N}}€Ð°Ð{\textperiodcentered}ие {\~{N}} помо{\~{N}}ˆ{\~{N}}{\OE}{\~{N}}{\v{Z}} {\~{N}}‚{\~{N}}€Ðµ{\~{N}}{\ldots} {\~{N}}€Ð°Ð{\textperiodcentered}ли{\~{N}}‡Ð½{\~{N}}‹{\~{N}}{\ldots} индеÐ{\textordmasculine}{\~{N}} ов по {\~{N}} е{\~{N}}€Ð¸{\~{N}} м {\~{N}}€ÐµÐ°Ð»{\~{N}}{\OE}н{\~{N}}‹{\~{N}}{\ldots} и модели{\~{N}}€Ð¾Ð²Ð°Ð½Ð½{\~{N}}‹{\~{N}}{\ldots} данн{\~{N}}‹{\~{N}}{\ldots}. Ð{\v{s}}аÐ{\P}д{\~{N}}‹Ð¹ индеÐ{\textordmasculine}{\~{N}} п{\~{N}}€Ð¾Ð°Ð½Ð°Ð»Ð¸Ð{\textperiodcentered}и{\~{N}}€Ð¾Ð²Ð°Ð½ дл{\~{N}} оп{\~{N}}€ÐµÐ´ÐµÐ»ÐµÐ½Ð¸{\~{N}} его Ð{\textperiodcentered}ави{\~{N}} имо{\~{N}} {\~{N}}‚и о{\~{N}}‚ дв{\~{N}}ƒ{\~{N}}{\ldots} Ð{\textordmasculine}омпонен{\~{N}}‚ {\~{N}}€Ð°Ð{\textperiodcentered}нооб{\~{N}}€Ð°Ð{\textperiodcentered}и{\~{N}} , бога{\~{N}}‚{\~{N}} {\~{N}}‚ва и в{\~{N}}‹{\~{N}}€Ð¾Ð²Ð½ÐµÐ½Ð½Ð¾{\~{N}} {\~{N}}‚и. Ин{\~{N}}„о{\~{N}}€Ð°{\~{N}}†Ð¸Ð¾Ð½Ð½Ð°{\~{N}} {\~{N}}„о{\~{N}}€Ð¼{\~{N}}ƒÐ»Ð° ІІІ{\~{N}} ннона H{\^{a}}€²= C{\^{I}}{\pounds} p i log2 p i на{\~{N}}{\ldots}оди{\~{N}}‚{\~{N}} {\~{N}} в линейной Ð{\textperiodcentered}ави{\~{N}} имо{\~{N}} {\~{N}}‚и о{\~{N}}‚ в{\~{N}}‹{\~{N}}€Ð¾Ð²Ð½ÐµÐ½Ð½Ð¾{\~{N}} {\~{N}}‚и и log2 о{\~{N}}‚ об{\~{N}}ˆÐµÐ³Ð¾ Ð{\textordmasculine}оли{\~{N}}‡Ðµ{\~{N}} {\~{N}}‚ва видов. ИндеÐ{\textordmasculine}{\~{N}} Симп{\~{N}} она D=1-{\^{a}}ˆ‘ n( n-1)/ N( N-1) и индеÐ{\textordmasculine}{\~{N}} Ð{\oe}аÐ{\textordmasculine}ин{\~{N}}‚о{\~{N}}ˆÐ° {\$}{\{}\backslashrm D{\}}{\^{}}{\{}\backslashprime{\}}={\{}\backslashtextstyle\backslashfrac{\{}{\{}\backslashrm N{\}}-\backslashsurd \backslashoverline{\{}\backslashSigma {\{}\backslashrm n{\}}{\_}{\{}{\{}\backslashrm i{\}}{\}}{\{}{\}}{\^{}}{\{}2{\}}{\}}{\}}{\{}{\{}\backslashrm N{\}}-\backslashsurd \backslashoverline{\{}{\{}\backslashrm N{\}}{\}}{\}}{\}}{\$} в{\~{N}}‹{\~{N}}€Ð°Ð{\P}енн{\~{N}}‹Ðµ{\~{N}}– в би{\~{N}}‚а{\~{N}}{\ldots}, на{\~{N}}{\ldots}од{\~{N}} {\~{N}}‚{\~{N}} {\~{N}} в линейной Ð{\textperiodcentered}ави{\~{N}} имо{\~{N}} {\~{N}}‚и о{\~{N}}‚ в{\~{N}}‹{\~{N}}€Ð¾Ð²Ð½ÐµÐ½Ð½Ð¾{\~{N}} {\~{N}}‚и и log2 о{\~{N}}‚ {\~{N}}‡Ð¸{\~{N}} ла видов. Ð{\v{z}}б{\~{N}} {\~{N}}ƒÐ{\P}да{\~{N}}{\v{Z}}{\~{N}}‚{\~{N}} {\~{N}} о{\~{N}}‚но{\~{N}}ˆÐµÐ½Ð¸{\~{N}} меÐ{\P}д{\~{N}}ƒ индеÐ{\textordmasculine}{\~{N}} ами и воÐ{\textperiodcentered}моÐ{\P}но{\~{N}} {\~{N}}‚и и{\~{N}}{\ldots} п{\~{N}}€Ð¸Ð¼ÐµÐ½ÐµÐ½Ð¸{\~{N}} .},
-annote = {ArticleType: research-article / Full publication date: 1975 / Copyright {\^{A}}{\textcopyright} 1975 Nordic Society Oikos},
-author = {DeJong, T. M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/DeJong - 1975 - A Comparison of Three Diversity Indices Based on Their Components of Richness and Evenness.pdf:pdf},
-isbn = {00301299},
-journal = {Oikos},
-number = {2},
-pages = {222--227},
-publisher = {Blackwell Publishing on behalf of Nordic Society Oikos},
-title = {{A Comparison of Three Diversity Indices Based on Their Components of Richness and Evenness}},
-url = {http://www.jstor.org/stable/3543712},
-volume = {26},
-year = {1975}
-}
-@article{Amzallag2001,
-abstract = {In plant physiology, data analysis is based on the comparison of mean values. In this perspective, variability around the mean value has no significance per se, but only for estimating statistical significance of the difference between two mean values. Another approach to variability is proposed here, derived from the difference between redundant and deterministic patterns of regulation in their capacity to buffer noise. From this point of view, analysis of variability enables the investigation of the level of redundancy of a regulation pattern, and even allows us to study its modifications. As an example, this method is used to investigate the effect of brassinosteroids (BSs) during vegetative growth in Sorghum bicolor. It is shown that, at physiological concentrations, BSs modulate the network of regulation without affecting the mean value. Thus, it is concluded that the physiological effect of BSs cannot be revealed by comparison of mean values. This example illustrates how a part of the reality (in this case, the most relevant one) is hidden by the classical methods of comparison between mean values. The proposed tools of analysis open new perspectives in understanding plant development and the nonlinear processes involved in its regulation. They also ask for a redefinition of fundamental concepts in physiology, such as growth regulator, optimality, stress and adaptation.},
-author = {Amzallag, G. N.},
-doi = {10.1046/j.1365-3040.2001.00742.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Amzallag - 2001 - Data analysis in plant physiology are we missing the reality.pdf:pdf},
-journal = {Plant Cell and Environment},
-number = {9},
-pages = {881--890},
-title = {{Data analysis in plant physiology: are we missing the reality?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-3040.2001.00742.x/abstract},
-volume = {24},
-year = {2001}
-}
-@article{Chen1999,
-abstract = {Ecologists and foresters are becoming increasingly aware of the importance of spatial information in ecosystem analysis and resource management. An across-scale analysis of forest structure was conducted to characterize the spatial characteristics of a 2 ha spruce-fir forest located inside Changbaishan Natural Reserve (CNR), PR China. The study was designed to develop an approach for assessment of within-stand heterogeneity to increase understanding of the effects of heterogeneity on pattern-process relationships in forests. Univariate and bivariate Ripley's K functions were employed to capture stand heterogeneity in terms of intra- and inter-specific point patterns of tree distributions. Stem-mapped crowns were generated and analyzed as canopy patches within a geographic information system (GIS) to quantify patterns within the strata of the forest canopy. The dominant spruces were randomly distributed within each height class bur aggregated when all height classes were analyzed. In addition, spruces had repulsive patterns to other species which exhibited clear aggregation. Canopy heterogeneity, both in terms of composition and spatial patterning, were complex-as expressed within canopy layers and among individual forest species. This across-scale complexity supports a multivariate spatial and across-scale approach to characterizing forest structure, and argues for linked pattern-process experiments. We suggest that joint field and simulation studies be conducted which relate changes in forest stand dynamics to changes in stand heterogeneity. These linked studies are needed to provide a measure of ecological significance relative to statistical significance of patterns. (C) 1999 Elsevier Science B.V. All rights reserved.},
-annote = {Article
-English
-FOREST ECOL MANAGE
-198HT},
-author = {Chen, JiQuan and Bradshaw, Gay A.},
-doi = {10.1016/S0378-1127(98)00543-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chen, Bradshaw - 1999 - Forest structure in space a case study of an old growth spruce-fir forest in Changbaishan Natural Reserve, PR Ch.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {219--233},
-title = {{Forest structure in space: a case study of an old growth spruce-fir forest in Changbaishan Natural Reserve, PR China}},
-url = {http://www.sciencedirect.com/science/article/pii/S037811279800543X},
-volume = {120},
-year = {1999}
-}
-@book{Illian2008,
-address = {Chichester},
-author = {Illian, Janine and Penttinen, Antti and Stoyan, Helga and Stoyan, Dietrich},
-booktitle = {Statistics in Practice},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Illian et al. - 2008 - Statistical Analysis and Modelling of Spatial Point Patterns.pdf:pdf},
-isbn = {0470014911, 9780470014912},
-pages = {1--534},
-publisher = {Wiley-Interscience},
-title = {{Statistical Analysis and Modelling of Spatial Point Patterns}},
-year = {2008}
-}
-@article{Blonder2014,
-abstract = {Aim The Hutchinsonian hypervolume is the conceptual foundation for many lines of ecological and evolutionary inquiry, including functional morphology, comparative biology, community ecology and niche theory. However, extant methods to sample from hypervolumes or measure their geometry perform poorly on high-dimensional or holey datasets. Innovation We first highlight the conceptual and computational issues that have prevented a more direct approach to measuring hypervolumes. Next, we present a new multivariate kernel density estimation method that resolves many of these problems in an arbitrary number of dimensions. Main conclusions We show that our method (implemented as the ‘hypervolume' R package) can match several extant methods for hypervolume geometry and species distribution modelling. Tools to quantify high-dimensional ecological hypervolumes will enable a wide range of fundamental descriptive, inferential and comparative questions to be addressed.},
-author = {Blonder, Benjamin and Lamanna, Christine and Violle, Cyrille and Enquist, Brian J.},
-doi = {10.1111/geb.12146},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blonder et al. - 2014 - The n-dimensional hypervolume.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-pages = {595--609},
-title = {{The n-dimensional hypervolume}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12146/full},
-volume = {23},
-year = {2014}
-}
-@misc{Gaigne2003,
-author = {Gaign{\'{e}}, Carl and Huiban, Jean-Pierre and Schmitt, Bertrand},
-booktitle = {mimeo},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gaign{\'{e}}, Huiban, Schmitt - 2003 - Labor Market and Industrial Location Evidence from French Data.pdf:pdf},
-keywords = {Gaign{\'{e}} (2003).pdf},
-mendeley-tags = {Gaign{\'{e}} (2003).pdf},
-title = {{Labor Market and Industrial Location: Evidence from French Data}},
-year = {2003}
-}
-@article{Wilkinson1983,
-abstract = {The paper is in two parts. Part I presents results of a Monte Carlo randomization study of Papadakis's covariance method of NN analysis which show that (i) a non-iterated Papadakis analysis tends to be conservatively biassed; (ii) iteration of the analysis as suggested by Bartlett (1978) leads to substantial positive bias in the treatment F ratio; (iii) the method is very inefficient when there are substantial trend effects in the data. A theoretical explanation of these results is given. Part II describes a new method of NN analysis discovered by the first author and developed in collaboration with the co-authors. The method is essentially a “moving-block” analogue of classical forms of analysis for “fixed” blocks (or rows, columns). It avoids the defects of Papadakis's method and leads to approximately unbiased analyses. It is nearly always and often substantially more efficient on average than classical analyses of complete or incomplete block experiments, and aiso more efficient than standard analyses of Latin or lattice square designs if there are appreciable row X column interactions in the data. New criteria of design for NN balance are described. Validity of the new method under randomization is demonstrated empirically with Monte Carlo studies.},
-author = {Wilkinson, G. N. and Eckert, S. R. and Hancock, T. W. and Mayo, O.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilkinson et al. - 1983 - Nearest Neighbour (NN) Analysis of Field Experiments.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {151--211},
-title = {{Nearest Neighbour (NN) Analysis of Field Experiments}},
-url = {https://www.jstor.org/stable/2345523},
-volume = {45},
-year = {1983}
-}
-@article{McGill2014,
-abstract = {Humans are transforming the biosphere in unprecedented ways, raising the important question of how these impacts are changing biodiversity. Here we argue that our understanding of biodiversity trends in the Anthropocene, and our ability to protect the natural world, is impeded by a failure to consider different types of biodiversity measured at different spatial scales. We propose that ecologists should recognize and assess 15 distinct categories of biodiversity trend. We summarize what is known about each of these 15 categories, identify major gaps in our current knowledge, and recommend the next steps required for better understanding of trends in biodiversity.},
-author = {McGill, Brian J. and Dornelas, Maria and Gotelli, Nicholas J. and Magurran, Anne E.},
-doi = {10.1016/j.tree.2014.11.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McGill et al. - 2014 - Fifteen forms of biodiversity trend in the Anthropocene.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {2},
-pages = {104--113},
-title = {{Fifteen forms of biodiversity trend in the Anthropocene}},
-url = {http://dx.doi.org/10.1016/j.tree.2014.11.006},
-volume = {30},
-year = {2014}
-}
-@article{McDonald2003,
-abstract = {Across eastern North America, there is a temporal trend from open Quercus forests to closed forests with increased Acer rubrum in the understory. We used a series of Ripley's K(d) analyses to examine changes in the spatial pattern of Quercus and Acer rubrum stems greater than 2.5 cm DBH over 45 yr in a 2-ha mapped stand. Specifically, we asked whether changes over time were consistent with the hypothesis that Quercus is being competitively replaced by Acer rubrum. Both Acer rubrum and Quercus stems are spatially clumped, but have become less clumped over time. Stem mortality from Hurricane Fran (1996) was more clumped in all strata of the forest, at all spatial scales, than expected if damage had occurred to stems at random. Acer rubrum ingrowth occurred more often near established trees (all species) in the midstory, whereas Quercus ingrowth occurred less often near established trees in the midstory. The specific hypothesis that stems of Acer rubrum in the midstory of the forest are associated with a lack of Quercus regeneration was strongly supported. This effect occurred at all spatial scales tested, including scales larger than that at which direct competition for light can occur. Edaphic gradients in the plot are correlated with many of the observed trends at large spatial scales, and our results suggest that the presence of such gradients can generate complex spatial patterns over time.},
-author = {McDonald, R. I. and Peet, Robert K. and Urban, D. L.},
-doi = {10.1658/1100-9233(2003)014[0441:SPOQRL]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McDonald, Peet, Urban - 2003 - Spatial pattern of Quercus regeneration limitation and Acer rubrum invasion in a Piedmont forest.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {441--450},
-title = {{Spatial pattern of Quercus regeneration limitation and Acer rubrum invasion in a Piedmont forest}},
-url = {http://www.bioone.org/doi/abs/10.1658/1100-9233(2003)014{\%}5B0441{\%}3ASPOQRL{\%}5D2.0.CO{\%}3B2},
-volume = {14},
-year = {2003}
-}
-@article{Ricotta2004,
-abstract = {The degree to which abundances are evenly divided among the species of a given community is a basic property of any biological community. Several evenness indices have thus far been proposed in ecological literature. However, despite their vast potential applicability in ecological research, none seems to be generally preferred. In this paper, I first summarize the basic requirements that evenness measures should meet to adequately behave in ecological studies. Then, I discuss the major drawbacks of these requirements and propose an alternative family of measures that are based on the notion of specificity used in fuzzy set theory for measuring the uncertainty associated with a fuzzy set.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: ABIOA
-PubMed ID: 15456986
-Language of Original Document: English
-Correspondence Address: Department of Plant Biology, University of Rome la Sapienza, Piazzale Aldo Moro 5, 00185 Rome, I.Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1023/B:ACBI.0000043438.41888.ac},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2004 - A recipe for unconventional evenness measures.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {2},
-pages = {95--104},
-title = {{A recipe for unconventional evenness measures}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-5444276557{\&}partnerID=40{\&}md5=342f8a7e088216542294d8919afd7091},
-volume = {52},
-year = {2004}
-}
-@article{Veech2005,
-abstract = {Insight into the factors that influence patterns of species diversity can be obtained by comparing real patterns to their counterparts derived under a model of randomness or a null model. For example, intraspecific aggregation is very common among a wide variety of protozoan, plant, and animal taxa. Despite this, ecologists do not yet fully appreciate the potential effect of intraspecific aggregation on patterns of species diversity. Intraspecific aggregation is predicted to limit alpha-diversity (mean species richness of a set of ecological communities) to a level less than that expected based on random distributions of individuals. Conversely, intraspecific aggregation should enhance beta-diversity (differences in species composition among communities). These effects on alpha- and beta-diversity should be related to the mean amount of intraspecific aggregation within a species assemblage (group of taxonomically similar species distributed among a set of communities). I tested these predictions by applying additive diversity partitioning and a randomization routine to 28 arthropod assemblages. Intraspecific aggregation was very common. It significantly limited alpha-diversity to less than that expected under the random model. At the same time, intraspecific aggregation enhanced beta-diversity. These effects were greatest in assemblages where intraspecific aggregation was greatest. The next step for ecologists is to identify those factors that cause conspecifics to aggregate and thus also influence patterns of species diversity.},
-author = {Veech, Joseph A},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veech - 2005 - Analyzing patterns of species diversity as departures from random expectations.pdf:pdf},
-isbn = {0030-1299},
-journal = {Oikos},
-number = {1},
-pages = {149--155},
-title = {{Analyzing patterns of species diversity as departures from random expectations}},
-volume = {108},
-year = {2005}
-}
-@article{Beguinot2015,
-abstract = {Aim: Register new species gradually becomes more difficult as sampling of a community progresses, addressing increasingly rarer species. Thus, although biodiversity assessments would ideally require complete samplings, only partial samplings are ordinarily achieved when species abundances distributions are highly heterogeneous within communities, which is often the case. Then, in the frequent context of partial samplings, answering knowingly whether to continue or stop an ongoing inventory require to tentatively assess the “profitability” of the extra sampling effort. That is, trying to estimate the number of species expected to be newly recorded thanks to a given further increase of the sampling size. Methods: Such estimate may be conveniently derived on the basis of the recorded numbers f1, f2, f3, fx, of species already recorded once, twice, three, {\ldots} x-times within the ongoing sampling. The derivation involves a Taylor expansion of the species accumulation curve, with the successive derivatives of the species accumulation curve being respectively expressed in terms of the successive recorded values of fx. Results: A simple nonparametric estimator of the expected number of newly recorded species is derived as a function of the foreseen additive sampling effort. Depending only upon the directly recorded values of the fx within the ongoing sampling, this estimator is easy-to-implement and, in particular, does not require recording explicitly the species accumulation curve. Conclusion: The practical interest of this estimator is to offer a convenient way to gauge the additional sampling effort required for a given increase in sample completeness, thus providing quantitative elements to determine whether further continuing an ongoing sampling looks appropriate or not, in the context of both limited available time expenditure and possible other competing priorities.},
-author = {B{\'{e}}guinot, Jean},
-doi = {10.9734/ARRB/2015/18809},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/B{\'{e}}guinot - 2015 - When Reasonably Stop Sampling How to Estimate the Gain in Newly Recorded Species According to the Degree of Supplement.pdf:pdf},
-journal = {Annual Research {\&} Review in Biology},
-number = {5},
-pages = {300--308},
-title = {{When Reasonably Stop Sampling? How to Estimate the Gain in Newly Recorded Species According to the Degree of Supplementary Sampling Effort}},
-url = {http://sciencedomain.org/abstract/10089},
-volume = {7},
-year = {2015}
-}
-@article{Rocchini2016,
-abstract = {HIGHLIGHTS • Invasive species can modify the struc-ture and function of ecosystems. • Reliable anticipation of species inva-sions relies on the quality of input data. • Sampling effort bias leads to an over-or under-estimation of species occur-rence. • We propose methods to consider sampling effort bias in species distri-bution modeling. • We demonstrate the power of incor-porating uncertainty in species distri-bution models. ABSTRACT Anticipating species distributions in space and time is necessary for effective biodiversity conservation and for prioritising management interventions. This is especially true when considering invasive species. In such a case, anticipating their spread is important to effectively plan management actions. However, considering uncertainty in the output of species distribution models is critical for correctly interpreting results and avoiding inappropriate decision-making. In particular, when dealing with species inventories, and avoiding inappropriate decision-making. In particular, when dealing with species inventories, the bias resulting from sampling effort may lead to an over-or under-estimation of the local density of occurrences of a species. In this paper we propose an innovative method to i) map sampling effort bias using cartogram models and ii) explicitly consider such uncertainty in the modeling procedure under a Bayesian framework, which allows the integration of multilevel input data with prior information to improve the anticipation of species distributions.},
-author = {Rocchini, Duccio and Garzon-Lopez, Carol X. and Marcantonio, Matteo and Amici, Valerio and Bacaro, Giovanni and Bastin, Lucy and Brummitt, Neil and Chiarucci, Alessandro and Foody, Giles M. and Hauffe, Heidi C. and He, Kate S. and Ricotta, Carlo and Rizzoli, Annapaola and Ros{\`{a}}, Roberto},
-doi = {10.1016/j.scitotenv.2016.12.038},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rocchini et al. - 2013 - Calculating landscape diversity with information-theory based indices A GRASS GIS solution.pdf:pdf},
-journal = {Science of the Total Environment},
-title = {{Anticipating species distributions: Handling sampling effort bias under a Bayesian framework}},
-url = {http://dx.doi.org/10.1016/j.scitotenv.2016.12.038},
-volume = {in press},
-year = {2016}
-}
-@article{Garnier2001,
-abstract = {1. The impact of sample preparation, rehydration procedure and time of collection on the determination of specific leaf area (SLA, the ratio of leaf area to leaf dry mass) and leaf dry matter content (LDMC, the ratio of leaf dry mass to fresh mass) of mature leaves was studied in three wild species growing in the field, chosen for their contrasting SLA and LDMC.2. Complete rehydration was achieved 6 h after samples were placed into water, but neither of the procedures tested-preparation of samples before rehydration or temperature applied during rehydration-had a significant effect on the final values of SLA or LDMC.3. As expected, water-saturated leaves had a lower LDMC than non-rehydrated leaves; more surprisingly, their SLA was also higher. The impact of rehydration on SLA was especially important when the SLA of the species was high.4. There was no significant effect of time of sampling on either trait in any species over the time period covered (09.00-16.30 h).5. These results suggest that SLA and LDMC obtained on water-saturated leaves (SLA(SAT) and LDMCSAT) can be used for species comparisons. We propose a standardized protocol for the measurement of these traits. This would allow for better consistency in data collection, a prerequisite for the constitution of large databases of functional traits.},
-author = {Garnier, Eric and Shipley, Bill and Roumet, Catherine and Laurent, G{\'{e}}rard},
-doi = {10.1046/j.0269-8463.2001.00563.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garnier et al. - 2001 - A standardized protocol for the determination of specific leaf area and leaf dry matter content.pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {688--695},
-title = {{A standardized protocol for the determination of specific leaf area and leaf dry matter content}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.0269-8463.2001.00563.x/abstract},
-volume = {15},
-year = {2001}
-}
-@phdthesis{Marcon2010a,
-author = {Marcon, Eric},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon - 2010 - Statistiques spatiales avec applications {\`{a}} l'{\'{e}}cologie et {\`{a}} l'{\'{e}}conomie.pdf:pdf},
-school = {AgroParisTech},
-title = {{Statistiques spatiales avec applications {\`{a}} l'{\'{e}}cologie et {\`{a}} l'{\'{e}}conomie}},
-year = {2010}
-}
-@phdthesis{Baraloto2001,
-author = {Baraloto, Christopher},
-publisher = {University of Michigan},
-title = {{Tradeoffs between neotropical tree seedling traits and performance in contrasting environments}},
-year = {2001}
-}
-@article{Clarke1998,
-abstract = {n multivariate analyses of the effects of both natural and anthropogenic environmental variability on community composition, many species are interchangeable in the way that they characterise the samples, giving rise to the concept of structural redundancy in community composition. Here, we develop a method of quantifying the extent of this redundancy by extracting a series of subsets of species, the multivariate response pattern of each of which closely matches that for the whole community. Structural redundancy is then reflected in the number of such subsets, which we term “response units”, that can be extracted without replacement. We have applied this technique to the effects of the Amoco-Cadiz oil-spill on marine macrobenthos in the Bay of Morlaix, France, and to the natural interannual variability of macrobenthos at two stations off the coast of Northumberland, England. Structural redundancy is shown to be remarkably high, with the number and sizes of subsets being comparable in all three examples. Taxonomic/functional groupings of species within the differing response units change in abundance in the same way over time. The response units are shown to possess a wide taxonomic spread and, using two different types of randomisation test, demonstrated to have a taxonomically and functionally coherent structure. The level of structural redundancy may therefore be an indirect measure of the resilience or compensation potential within an assemblage.},
-author = {Clarke, K. R. and Warwick, R. M.},
-doi = {10.1007/s004420050379},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clarke, Warwick - 1998 - Quantifying structural redundancy in ecological communities.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {278--289},
-title = {{Quantifying structural redundancy in ecological communities}},
-url = {http://link.springer.com/article/10.1007/s004420050379},
-volume = {113},
-year = {1998}
-}
-@article{Mittelbach2015,
-abstract = {Ecologists often view community assembly as a process involving the dispersal of species from a static regional species pool followed by environmental filtering to establish the local community. This conceptual framework ignores the dynamic nature of species pools and fails to recognize that communities are assembled by processes operating over a vast range of temporal and spatial scales. Species pool richness and composition are influenced by metacommunity dynamics over short timescales and by speciation, extinction, and dispersal over long timescales. We suggest that a stronger focus on the geography of speciation, the formation of secondary sympatry, and the feedback between local and regional processes is needed to fully understand community assembly and the importance of dynamic species pools.},
-author = {Mittelbach, Gary G. and Schemske, Douglas W.},
-doi = {10.1016/j.tree.2015.02.008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mittelbach, Schemske - 2015 - Ecological and evolutionary perspectives on community assembly.pdf:pdf},
-journal = {Trends in Ecology and Evolution},
-number = {5},
-pages = {241--247},
-title = {{Ecological and evolutionary perspectives on community assembly}},
-url = {http://dx.doi.org/10.1016/j.tree.2015.02.008},
-volume = {30},
-year = {2015}
-}
-@article{Anselin1995,
-abstract = {The capabilities for visualization, rapid data retrieval, and manipulation in geographic information systems (GIS) have created the need for new techniques of exploratory data analysis that focus on the “spatial” aspects of the data. The identification of local patterns of spatial association is an important concern in this respect. In this paper, I outline a new general class of local indicators of spatial association (LISA) and show how they allow for the decomposition of global indicators, such as Moran's I, into the contribution of each observation. The LISA statistics serve two purposes. On one hand, they may be interpreted as indicators of local pockets of nonstationarity, or hot spots, similar to the Gi and G*i statistics of Getis and Ord (1992). On the other hand, they may be used to assess the influence of individual locations on the magnitude of the global statistic and to identify “outliers,” as in Anselin's Moran scatterplot (1993a). An initial evaluation of the properties of a LISA statistic is carried out for the local Moran, which is applied in a study of the spatial pattern of conflict for African countries and in a number of Monte Carlo simulations.},
-author = {Anselin, Luc},
-doi = {10.1111/j.1538-4632.1995.tb00338.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anselin - 1995 - Local Indicators of Spatial Association - LISA.pdf:pdf},
-journal = {Geographical Analysis},
-number = {2},
-pages = {93--115},
-title = {{Local Indicators of Spatial Association - LISA}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1995.tb00338.x/abstract},
-volume = {27},
-year = {1995}
-}
-@article{Auerbach1987,
-abstract = {Traditional ecological theory has stressed the importance of competitive interactions in regulating species richness. Recent research has transcended this viewpoint by considering the role of stochastic processes, mosaic phenomena and nonequilibrium conditions in the regulation of richness. This growing body of work indicates that the determinants of plant species richness may vary predictably over different spatial scales.},
-author = {Auerbach, Michael and Shmida, Avi},
-doi = {10.1016/0169-5347(87)90005-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Auerbach, Shmida - 1987 - Spatial scale and the determinants of plant species richness.pdf:pdf},
-isbn = {0169-5347},
-issn = {0169-5347},
-journal = {Trends in Ecology {\&} Evolution},
-number = {8},
-pages = {238--42},
-pmid = {21227857},
-title = {{Spatial scale and the determinants of plant species richness.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/21227857},
-volume = {2},
-year = {1987}
-}
-@article{Condit2002,
-abstract = {The high alpha-diversity of tropical forests has been amply documented, but beta-diversity-how species composition changes with distance has seldom been studied. We present quantitative estimates of beta-diversity for tropical trees by comparing species composition of plots in lowland terra firme forest in Panama, Ecuador, and Peru. We compare observations with predictions derived from a neutral model in which habitat is uniform and only dispersal and speciation influence species turnover. We find that beta-diversity is higher in Panama than in western Amazonia and that patterns in both areas are inconsistent with the neutral model. In Panama, habitat variation appears to increase species turnover relative to Amazonia, where unexpectedly tow turnover over great distances suggests that population densities of some species are bounded by as yet unidentified processes. At intermediate scales in both regions, observations can be matched by theory, suggesting that dispersal limitation, with speciation, influences species turnover.},
-annote = {ISI Document Delivery No.: 516PD
-Times Cited: 344
-Cited Reference Count: 17
-AMER ASSOC ADVANCEMENT SCIENCE},
-author = {Condit, Richard and Pitman, Nigel and Leigh, Egbert G. Jr and Chave, J{\'{e}}r{\^{o}}me and Terborgh, John and Foster, Robin B. and N{\'{u}}{\~{n}}ez, Percy and Aguilar, Salom{\'{o}}n and Valencia, Renato and Villa, Gorky and Muller-Landau, Helene C. and Losos, Elizabeth and Hubbell, Stephen P.},
-doi = {10.1126/science.1066854},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Condit et al. - 2002 - Beta-diversity in tropical forest trees.pdf:pdf},
-journal = {Science},
-number = {5555},
-pages = {666--669},
-title = {{Beta-diversity in tropical forest trees}},
-url = {http://science.sciencemag.org/content/295/5555/666/},
-volume = {295},
-year = {2002}
-}
-@misc{Baker2015,
-abstract = {This selective review of the Quaternary paleoclimate of the South American summer monsoon (SASM) domain presents viewpoints regarding a range of key issues in the field, many of which are unresolved and some of which are controversial. (1) El Ni{\~{n}}o-Southern Oscillation variability, while the most important global-scale mode of interannual climate variation, is insufficient to explain most of the variation of tropical South American climate observed in both the instrumental and the paleoclimate records. (2) Significant climate variation in tropical South America occurs on seasonal to orbital (i.e. multi-millennial) time scales as a result of sea-surface temperature (SST) variation and ocean-atmosphere interactions of the tropical Atlantic. (3) Decadal-scale climate variability, linked with this tropical Atlantic variability, has been a persistent characteristic of climate in tropical South America for at least the past half millennium, and likely, far beyond. (4) Centennial-to-millennial climate events in tropical South America were of longer duration and, perhaps, larger amplitude than any observed in the instrumental period, which is little more than a century long in tropical South America. These were superimposed upon both precession-paced insolation changes that caused significant variation in SASM precipitation and eccentricity-paced global glacial boundary conditions that caused significant changes in the tropical South American moisture balance. As a result, river sediment and water discharge increased and decreased across tropical South America, lake levels rose and fell, paleolakes arose and disappeared on the Altiplano, glaciers waxed and waned in the tropical Andes, and the tropical rainforest underwent significant changes in composition and extent.To further evaluate climate forcing over the last glacial cycle ({\~{}}125ka), we developed a climate forcing model that combines summer insolation forcing and a proxy for North Atlantic SST forcing to reconstruct long-term precipitation variation in the SASM domain. The success of this model reinforces our confidence in assigning causation to observed reconstructions of precipitation. In addition, we propose a critical correction for speleothem stable oxygen isotopic ratios, which are among the most significant of paleoclimate proxies in tropical South America for reconstruction of variation of paleo-precipitation (or SASM intensity). However, it is already well known that any particular $\delta$18O value observed in speleothem carbonate is affected by two processes that have nothing to do with changes in precipitation amount-the influence of temperature on carbonate-water isotopic fractionation in the cave and the influence of changing $\delta$18O of seawater. Quantitatively accounting for both "artifacts" can significantly alter the interpretations of speleothem records. In tropical South America, both adjustments act in the same direction and have the tendency to increase the true amplitude of the paleo-hydrologic signal (but by different amounts in glacial and inter-glacial stages). These corrections have even graver implications for the interpretation of tropical Northern Hemisphere speleothem records (e.g. Chinese speleothems) where the combined adjustments tend to decrease or even eliminate the "true" signal amplitude.},
-author = {Baker, Paul A. and Fritz, Sherilyn C.},
-booktitle = {Quaternary Science Reviews},
-doi = {10.1016/j.quascirev.2015.06.011},
-pages = {31--47},
-title = {{Nature and causes of Quaternary climate variation of tropical South America}},
-volume = {124},
-year = {2015}
-}
-@article{Leinster2012,
-abstract = {Realistic measures of biodiversity should reflect not only the relative abundances of species, but also the differences between them. We present a natural family of diversity measures taking both factors into account. This is not just another addition to the already long list of diversity indices: instead, a single formula subsumes many of the most popular indices, including Shannon's, Simpson's, species richness, and Rao's quadratic entropy. These popular indices can then be used and understood in a unified way, and the relationships between them are made plain. The new measures are, moreover, effective numbers, so that percentage changes and ratio comparisons of diversity value are meaningful. We advocate the use of diversity profiles, which provide a faithful graphical represen- tation of the shape of a community; they show how the perceived diversity changes as the emphasis shifts from rare to common species. Communities can usefully be compared by comparing their diversity profiles. We show by example that this is a far more subtle method than any relying on a single statistic. Some ecologists view diversity indices with suspicion, questioning whether they are biologically meaningful. By dropping the naive assumption that distinct species have nothing in common, working with effective numbers, and using diversity profiles, we arrive at a system of diversity measurement that should lay much of this suspicion to rest.},
-author = {Leinster, Tom and Cobbold, Christina},
-doi = {10.1890/10-2402.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leinster, Cobbold - 2012 - Measuring diversity the importance of species similarity.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {477--489},
-title = {{Measuring diversity: the importance of species similarity}},
-url = {http://dx.doi.org/10.1890/10-2402.1},
-volume = {93},
-year = {2012}
-}
-@article{Chown2004,
-author = {Chown, S. L. and Gaston, Kevin J. and Robinson, D.},
-doi = {10.1111/j.0269-8463.2004.00825.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chown, Gaston, Robinson - 2004 - Macrophysiology large-scale patterns in physiological traits and their ecological implications.pdf:pdf},
-journal = {Functional Ecology},
-number = {2},
-pages = {159--167},
-title = {{Macrophysiology: large-scale patterns in physiological traits and their ecological implications}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0269-8463.2004.00825.x/abstract},
-volume = {18},
-year = {2004}
-}
-@article{Bourguignon1979,
-abstract = {A decomposable inequality measure is defined as a measure such that the total inequality of a population can be broken down into a weighted average of the inequality existing within subgroups of the population and the inequality existing between them. Thus, decomposable measures differ only by the weights given to the inequality within the subgroups of the population. It is proven that the only zero-homogeneous "income-weighted" decomposable measure is Theil's coefficient (T) and that the only zero-homogeneous "population-weighted" decomposable measure is the logarithm of the arithmetic mean over the geometric mean (L). More generally, it is proved that T and L are the only decomposable inequality measures such that the weight of the "within-components" in the total inequality of a partitioned population sum to a constant. More general decomposable measures are also analyzed.},
-author = {Bourguignon, Fran{\c{c}}ois},
-doi = {10.2307/1914138},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bourguignon - 1979 - Decomposable Income Inequality Measures.pdf:pdf},
-journal = {Econometrica},
-number = {4},
-pages = {901--920},
-title = {{Decomposable Income Inequality Measures}},
-url = {https://www.jstor.org/stable/1914138},
-volume = {47},
-year = {1979}
-}
-@article{Hlavinka2013,
-abstract = {Leaf chlorophyll content is an important physiological parameter which can serve as an indicator of nutritional status, plant stress or senescence. Signals proportional to the chlorophyll content can be measured non-destructively with instruments detecting leaf transmittance (e.g., SPAD-502) or reflectance (e.g., showing normalized differential vegetation index, NDVI) in red and near infrared spectral regions. The measurements are based on the assumption that only chlorophylls absorb in the examined red regions. However, there is a question whether accumulation of other pigments (e.g., anthocyanins) could in some cases affect the chlorophyll meter readings. To answer this question, we cultivated tomato plants (Solanum lycopersicum L.) for a long time under low light conditions and then exposed them for several weeks (4 h a day) to high sunlight containing the UV-A spectral region. The senescent leaves of these plants evolved a high relative content of anthocyanins and visually revealed a distinct blue color. The SPAD and NDVI data were collected and the spectra of diffusive transmittance and reflectance of the leaves were measured using an integration sphere. The content of anthocyanins and chlorophylls was measured analytically. Our results show that SPAD and NDVI measurement can be significantly affected by the accumulated anthocyanins in the leaves with relatively high anthocyanin content. To describe theoretically this effect of anthocyanins, concepts of a specific absorbance and a leaf spectral polarity were developed. Corrective procedures of the chlorophyll meter readings for the anthocyanin contribution are suggested both for the transmittance and reflectance mode.},
-author = {Hlavinka, Jan and Nau{\v{s}}, Jan and {\v{S}}pundov{\'{a}}, Martina},
-doi = {10.1007/s11120-013-9934-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hlavinka, Nau{\v{s}}, {\v{S}}pundov{\'{a}} - 2013 - Anthocyanin contribution to chlorophyll meter readings and its correction.pdf:pdf},
-journal = {Photosynthesis Research},
-number = {3},
-pages = {277--295},
-title = {{Anthocyanin contribution to chlorophyll meter readings and its correction}},
-url = {http://dx.doi.org/10.1007/s11120-013-9934-y},
-volume = {118},
-year = {2013}
-}
-@book{Briggs2009,
-author = {Briggs, Jason R. and Weinachter, Michel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Briggs, Weinachter - 2009 - Domptage de serpent pour les enfants. Apprendre {\`{a}} programmer avec Python.pdf:pdf},
-title = {{Domptage de serpent pour les enfants. Apprendre {\`{a}} programmer avec Python}},
-url = {http://www.briggs.net.nz/log/writing/snake-wrangling-for-kids},
-year = {2009}
-}
-@article{Izsak1996,
-abstract = {The author previously described special sensitivity measures for diversity indices. These measures make possible on analytical treatment of the index sensitivity. In the article a detailed analysis of sensitivity properties of the Hurlbert indices is presented. In the first step the abundances nk were sequenced in an increasing order. Plotting the sensitivity against nk or log nk, essential sensitivity properties can be observed. For example, one can study the sensitivities to changes in the dominant and subdominant abundances, the site of the “nearly neutral” abundance and the site of local sensitivity maxima in the domain of the relatively rare categories. The observations are supported by mathematical reasoning.},
-author = {Izs{\'{a}}k, J{\'{a}}nos},
-doi = {10.1002/bimj.4710380804},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Izs{\'{a}}k - 1996 - Sensitivity Profiles of Diversity Indices.pdf:pdf},
-journal = {Biometrical Journal},
-number = {8},
-pages = {921--930},
-title = {{Sensitivity Profiles of Diversity Indices}},
-url = {http://dx.doi.org/10.1002/bimj.4710380804},
-volume = {38},
-year = {1996}
-}
-@incollection{Hubbell1986,
-abstract = {When a tree falls in the forest, the canopy hole or light gap it creates sets in motion a chain of events known as gap-phase regeneration which culminates in the replacement of the previous canopy tree by a new one. Gap disturbances provide the principal or only means by which most tree species can maintain their representation in closed-canopy forests. Therefore understanding the gap disturbance regime and knowing the rules of tree by tree regeneration processess are fundamental to understanding the structure and dynamics of closed canopy tree communities. Regeneration guilds: primary tree spp; early pioneer spp, and late secondary spp. Tree adjacent to gap or which stand above the surrounding canopy suffer a greater risk of falling than trees which are surrounded by plants as tall or taller than themselves},
-author = {Hubbell, Stephen P. and Foster, Robin B.},
-booktitle = {Plant Ecology},
-isbn = {1355},
-pages = {77--96},
-title = {{Canopy gaps and the dynamics of a neotropical forest}},
-year = {1986}
-}
-@article{Alonso-Villar2002,
-abstract = {There is no doubt that people like to migrate to large cities because they can acquire a wider range of products and jobs, but also because they can more easily exchange information and ideas. In this respect, we attempt to explain the formation of metropolitan areas by using a general equilibrium model, in which concentration emerges not only from interaction between in- creasing returns to scale at firmlevel, transport costs and labor mobility, but also fromhuman capital externalities. This paper shows that there is new scope for government activity.},
-author = {Alonso-Villar, Olga},
-doi = {10.1007/s001680200090},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alonso-Villar - 2002 - Urban agglomeration Knowledge spillovers and product diversity.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {4},
-pages = {551--573},
-title = {{Urban agglomeration: Knowledge spillovers and product diversity}},
-url = {https://link.springer.com/article/10.1007/s001680200090},
-volume = {36},
-year = {2002}
-}
-@article{Gosselin2006,
-abstract = {Evenness is the component of species diversity that was built to be mathematically independent from species richness. Yet, earlier work questioned the generality of this independence. However, this earlier work involved only a few relative abundance distributions (RADs), very limited gradients of species richness, or evenness indices, such as Pielou's index, that were not defined in relation to a precise, coherent set of axioms. We show that for very different theoretical RADs, a relationship between evenness indices and species richness does exist and is strong-at least for some RADs and/or when species richness is under 20. Furthermore, this relationship is mostly negative, which contradicts some previous studies. We also show that, for the very uneven RADs we tested, evenness indices depend even more on species richness than diversity indices do. Finally, we discuss the philosophy behind the analysis of evenness-richness relationships within and between RADs, as well as the interest of correcting evenness indices for species richness when species richness varies, especially with many values under 20. (c) 2006 Elsevier Ltd. All rights reserved.},
-annote = {Gosselin, Ferderic},
-author = {Gosselin, Fr{\'{e}}d{\'{e}}ric},
-doi = {10.1016/j.jtbi.2006.04.017},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gosselin - 2006 - An assessment of the dependence of evenness indices on species richness.pdf:pdf},
-isbn = {0022-5193},
-journal = {Journal of Theoretical Biology},
-number = {3},
-pages = {591--597},
-title = {{An assessment of the dependence of evenness indices on species richness}},
-volume = {242},
-year = {2006}
-}
-@article{Diggle2007,
-abstract = {Methods for the statistical analysis of stationary spatial point process data are now well established, methods for nonstationary processes less so. One of many sources of nonstationary point process data is a case-control study in environmental epidemiology. In that context, the data consist of a realization of each of two spatial point processes representing the locations, within a specified geographical region, of individual cases of a disease and of controls drawn at random from the population at risk. In this article, we extend work by Baddeley, Moller, and Waagepetersen (2000, Statistica Neerlandica 54, 329-350) concerning estimation of the second-order properties of a nonstationary spatial point process. First, we show how case-control data can be used to overcome the problems encountered when using the same data to estimate both a spatially varying intensity and second-order properties. Second, we propose a semiparametric method for adjusting the estimate of intensity so as to take account of explanatory variables attached to the cases and controls. Our primary focus is estimation, but we also propose a new test for spatial clustering that we show to be competitive with existing tests. We describe an application to an ecological study in which juvenile and surviving adult trees assume the roles of controls and cases.},
-annote = {Diggle, P. J. Gomez-Rubio, V. Brown, P. E. Chetwynd, A. G. Gooding, S.},
-author = {Diggle, Peter J. and G{\'{o}}mez-Rubio, V. and Brown, P. E. and Chetwynd, A. G. and Gooding, S.},
-doi = {10.1111/j.1541-0420.2006.00683.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle et al. - 2007 - Second-order analysis of inhomogeneous spatial point processes using case-control data.pdf:pdf},
-journal = {Biometrics},
-number = {2},
-pages = {550--557},
-title = {{Second-Order Analysis of Inhomogeneous Spatial Point Processes Using Case-Control Data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2006.00683.x/abstract},
-volume = {63},
-year = {2007}
-}
-@article{Picard2002,
-abstract = {Is a negative spatial correlation between basal area and its increment indicative of tree competition, in a forest stand considered as a realisation of a point process? For a bivariate point process, the spatial correlation results from two components: the value of the marks and tree positions, and a negative spatial correlation can occur without any correlation between the marks knowing their type. In a forest stand in French Guiana, a negative spatial correlation is observed. Moreover, the big trees exhibit a regular pattern, independently from the small trees that are clustered. This configuration is sufficient to explain the negative correlation without involving competition. Competition however remains as a process that explains the shift from clustering to regularity with an increasing tree size.},
-author = {Picard, Nicolas and Bar-Hen, Avner},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Picard, Bar-Hen - 2002 - Is the spatial correlation between the tree basal area and its increment a good indicator for competition.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {1},
-pages = {41--51},
-title = {{Is the spatial correlation between the tree basal area and its increment a good indicator for competition?}},
-volume = {59},
-year = {2002}
-}
-@article{Kempton1976,
-annote = {10.1038/262818a0
-10.1038/262818a0},
-author = {Kempton, R. A. and Taylor, L. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kempton, Taylor - 1976 - Models and statistics for species diversity.pdf:pdf},
-journal = {Nature},
-number = {5571},
-pages = {818--820},
-title = {{Models and statistics for species diversity}},
-url = {http://dx.doi.org/10.1038/262818a0},
-volume = {262},
-year = {1976}
-}
-@article{Garg2016,
-abstract = {In this paper, we define parametric R-norm directed-divergence convex function and discuss their special cases and prove some properties similar to Kullback–Leibler information measure. From R-norm divergence measure new information measures have also been derived and their relations with different measures of entropy have been obtained and give its application in industrial engineering.},
-author = {Garg, Dhanesh and Kumar, Satish},
-doi = {10.1142/S0219025716500144},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garg, Kumar - 2016 - Parametric R-norm directed-divergence convex function.pdf:pdf},
-issn = {0219-0257},
-journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics},
-number = {2},
-pages = {1650014},
-title = {{Parametric R-norm directed-divergence convex function}},
-url = {http://www.worldscientific.com/doi/10.1142/S0219025716500144},
-volume = {19},
-year = {2016}
-}
-@article{Simpson1949,
-author = {Simpson, E. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Simpson - 1949 - Measurement of diversity.pdf:pdf},
-journal = {Nature},
-number = {4148},
-pages = {688},
-title = {{Measurement of diversity}},
-volume = {163},
-year = {1949}
-}
-@article{Getis1984,
-abstract = {After the author has reviewed second-order theory for map-pattern analysis, he sets forth an approach for the study of interaction where spatial structure is implicitly built into various pattern models. The models are models of clustering when all members of the cluster are centered at one point. A density analysis is proposed where spatial autocorrelation may be discerned. An example using population distribution in East Anglia, 1971, is given along with comparisons to a central place model.},
-author = {Getis, Arthur},
-doi = {10.1068/a160173},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Getis - 1984 - Interaction modeling using second-order analysis(2).pdf:pdf},
-journal = {Environment and Planning A},
-pages = {173--183},
-title = {{Interaction modeling using second-order analysis}},
-url = {http://journals.sagepub.com/doi/abs/10.1068/a160173?journalCode=epna},
-volume = {16},
-year = {1984}
-}
-@article{Yakovenko2009,
-abstract = {This Colloquium reviews statistical models for money, wealth, and income distributions developed in the econophysics literature since the late 1990s. By analogy with the Boltzmann-Gibbs distribution of energy in physics, it is shown that the probability distribution of money is exponential for certain classes of models with interacting economic agents. Alternative scenarios are also reviewed. Data analysis of the empirical distributions of wealth and income reveals a two-class distribution. The majority of the population belongs to the lower class, characterized by the exponential ("thermal") distribution, whereas a small fraction of the population in the upper class is characterized by the power-law ("superthermal") distribution. The lower part is very stable, stationary in time, whereas the upper part is highly dynamical and out of equilibrium.},
-archivePrefix = {arXiv},
-arxivId = {0905.1518},
-author = {Yakovenko, Victor M. and Rosser, J. Barkley},
-doi = {10.1103/RevModPhys.81.1703},
-eprint = {0905.1518},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yakovenko, Rosser - 2009 - Colloquium Statistical mechanics of money, wealth, and income.1518:1518},
-journal = {arXiv},
-number = {v2},
-title = {{Colloquium: Statistical mechanics of money, wealth, and income}},
-url = {http://arxiv.org/abs/0905.1518},
-volume = {0905.1518},
-year = {2009}
-}
-@techreport{McFadden1977,
-abstract = {The overall objective of the Urban Travel Demand Forecasting Project is to provide transportation engineers and planners with the information necessary to select and use policy-oriented disaggregate behavioral travel demand models, and to assess the applicability and limits of specific alternative models. This volume is devoted to the investigations of demand, forming the core of this project.},
-address = {San Francisco},
-author = {McFadden, Daniel and Talvitie, A. P. and and Associates},
-publisher = {The Institute of Transportation Studies, University of California, Berkeley and Irvine},
-title = {{Demand Model Estimation and Validation}},
-url = {http://elsa.berkeley.edu/users/mcfadden/utdfp5.html},
-year = {1977}
-}
-@article{Bar-Hen2006,
-abstract = {The spatial distributions of two species of tree result in a bivariate pattern. This pattern characterizes biological mechanism involved within a for- est with the spatial localization of the trees. If we consider simultaneously two species, the main question is not to describe the marginal distribution of each species but to describe the relationship between the repartitions of the two spe- cies under study. The relationship between two clouds of points can be described in various ways and therefore many indices can be defined. Each index will give a specific information about these relationships and will greatly depends on the ecological mechanisms, i.e., the point process that leads to the observed repartition. The aim of this article is to review the leading indices in ecology and to provide guidelines for practical use. To mimic ecological situations, we simulated 13 point process that can model classical relationships between two species of trees and compute nine classical indices. The interest of the various indices are discussed. A R package for simulating the point process and to com- pute the indices is available on request. The package is available upon request at picard@cirad.fr or avner@inapg.fr},
-author = {Bar-Hen, Avner and Picard, Nicolas},
-doi = {10.1007/s00180-006-0008-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bar-Hen, Picard - 2006 - Simulation study of dissimilarity between point process.pdf:pdf},
-journal = {Computational Statistics},
-number = {3-4},
-pages = {487--507},
-title = {{Simulation study of dissimilarity between point process}},
-url = {http://link.springer.com/10.1007/s00180-006-0008-x},
-volume = {21},
-year = {2006}
-}
-@incollection{Margalef1958a,
-address = {Berkeley, California},
-author = {Margalef, Ramon},
-booktitle = {Perspectives in Marine Biology},
-editor = {Buzzati-Traverso, A.A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Margalef - 1958 - Information theory in ecology.pdf:pdf},
-pages = {323--349},
-publisher = {University of California Press},
-title = {{Temporal Succession and Spatial Heterogeneity in Phytoplankton}},
-url = {https://books.google.co.in/books?id=XNKPMwEACAAJ},
-year = {1958}
-}
-@article{Holste1998,
-abstract = {The order- q Tsallis {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img5.gif] and R{\'{e}}nyi entropy {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img6.gif] receive broad applications in the statistical analysis of complex phenomena. A generic problem arises, however, when these entropies need to be estimated from observed data. The finite size of data sets can lead to serious systematic and statistical errors in numerical estimates. In this paper, we focus upon the problem of estimating generalized entropies from finite samples and derive the Bayes estimator of the order- q Tsallis entropy, including the order-1 (i.e. the Shannon) entropy, under the assumption of a uniform prior probability density. The Bayes estimator yields, in general, the smallest mean-quadratic deviation from the true parameter as compared with any other estimator. Exploiting the functional relationship between {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img7.gif] and {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img8.gif] , we use the Bayes estimator of {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img7.gif] to estimate the R{\'{e}}nyi entropy {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img8.gif] . We compare these novel estimators with the frequency-count estimators for {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img7.gif] and {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0305-4470/31/11/007/img8.gif] . We find by numerical simulations that the Bayes estimator reduces statistical errors of order- q entropy estimates for Bernoulli as well as for higher-order Markov processes derived from the complete genome of the prokaryote Haemophilus influenzae .},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Holste, D. and Gro{\ss}e, I. and Herzel, H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holste, Gro{\ss}e, Herzel - 1998 - Bayes' estimators of generalized entropies.pdf:pdf},
-journal = {Journal of Physics A: Mathematical and General},
-number = {11},
-pages = {2551--2566},
-title = {{Bayes' estimators of generalized entropies}},
-url = {http://stacks.iop.org/0305-4470/31/i=11/a=007},
-volume = {31},
-year = {1998}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2008,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n° 2008-1136 du 3 novembre 2008 modifiant le d{\'{e}}cret n° 2002-634 du 29 avril 2002 portant cr{\'{e}}ation du compte {\'{e}}pargne-temps dans la fonction publique de l'Etat et dans la magistrature et indemnisant des jours acccumul{\'{e}}s sur le compte {\'{e}}pargne-temps de}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000019723547},
-year = {2008}
-}
-@article{Fehmi2001,
-abstract = {Spatial data can provide much information about the interrelations of plants and the relationship between individuals and the environment. Spatially ambiguous plants, i.e. plants without readily identifiable loci, and plants that are profusely abundant, present non-trivial impediments to the collection and analysis of vegetation data derived from standard spatial sampling techniques. Sampling with grids of presence/absence quadrats can ameliorate much of this difficulty. Our analysis of 10 fully-mapped Nassella pulchra- dominated grassland plots demonstrates the applicability of the grid-based approach which revealed spatial dependence at a much lower sampling effort than mapping each plant. Ripley's K- function, a test commonly used for point patterns, was effective for pattern analysis on the grids and the gridded quadrat technique was an effective tool for quantifying spatial patterns. The addition of spatial pattern measures should allow for better comparisons of vegetation structure between sites, instead of sole reliance on species composition data.},
-author = {Fehmi, Jeffrey S. and Bartolome, James W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fehmi, Bartolome - 2001 - A grid-based method for sampling and analysing spatially ambiguous plants.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {467--472},
-title = {{A grid-based method for sampling and analysing spatially ambiguous plants}},
-url = {www.jstor.org/stable/3236998},
-volume = {12},
-year = {2001}
-}
-@article{terBraak1983,
-abstract = {Attention is drawn to some useful but not generally known properties of principal components analysis (PCA). Noncentered PCA of proportion data gives site ordinations that display approximate alpha diversities of sites and beta diversities of groups of sites, as measured by the Simpson index and mean squared Euclidean distance, respectively. Species centering allows a better approximation to beta diversities. Alpha diversities can still be visualized after centering if the true origin is projected into the plane of the ordination. The approximate species composition of each site can also be visualized if the site ordination is combined with a species ordination. The resulting plot of site scores and species loadings is called a PCA biplot. Finally, in a PCA biplot that displays both species composition and diversity, diversity values can be explained in terms of the main species contributing to diversity. In such a biplot the sum of squares of the species loadings must be scaled to unity, while the site scores must be scaled to a sum of squares equal to the corresponding eigenvalue. This type of biplot is termed a @'distance biplot.@' For a simple illustration noncentered and species-centered distance biplots were produced for some diatom samples taken from Dutch moorland pools in the 1920s and 1978. The distance biplot is concluded to be among the most powerful analytical tools for species-composition data and derives some of its power from properties not possessed by, for example, reciprocal averaging. One problem is that it attaches little weight to rare species, but this problem can be solved by various possible data transformations based on the theory of diversity indices.},
-author = {ter Braak, Cajo J. F.},
-doi = {10.2307/1939964},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/ter Braak - 1983 - Principal components biplots and alpha and beta diversity.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {454--462},
-title = {{Principal components biplots and alpha and beta diversity}},
-url = {http://www.jstor.org/stable/1939964},
-volume = {64},
-year = {1983}
-}
-@article{Yamada2004,
-abstract = {The network and planar K-function methods are applied to traffic accident data to illustrate the risk of false positive detection associated with the use of a statistic designed for a planar space to analyze a network-constrained phenomenon. We also demonstrate the benefits of using a method specifically designed for a network space. The results clearly indicate that the planar K-function analysis is problematic since it entails a significant chance of over-detecting clustered patterns. Analyses are implemented based on Monte Carlo simulation and applied to 1997 traffic accident data in the Buffalo, NY area.},
-author = {Yamada, Ikuho and Thill, Jean-Claude},
-doi = {10.1016/j.jtrangeo.2003.10.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yamada, Thill - 2004 - Comparison of planar and network K-functions in traffic accident analysis.pdf:pdf},
-journal = {Journal of Transport Geography},
-number = {2},
-pages = {149--158},
-title = {{Comparison of planar and network K-functions in traffic accident analysis}},
-volume = {12},
-year = {2004}
-}
-@article{Scheiner2017,
-abstract = {We present a framework for biodiversity metrics that organizes the growing panoply of metrics. Our framework distinguishes metrics based on the type of information–abundance, phylogeny, function–and two common properties–magnitude and variability. Our new metrics of phylogenetic diversity are based on a partition of the total branch lengths of a cladogram into the proportional share of each species, including: a measure of divergence which standardizes the amount of evolutionary divergence by species richness and time depth of the cladogram; a measure of regularity which is maximal when the tree is perfectly symmetrical so that all species have the same proportional branch lengths; a measure that combines information on the magnitude and variability of abundance with phylogenetic variability, and a measure of phylogenetically weighted effective mean abundance; and indicate how those metrics can be decomposed into $\alpha$ and $\beta$ components. We illustrate the utility of these new metrics using empirical data on the bat fauna of Manu, Peru. Divergence was greatest in lowland rainforest and at the transition between cloud and elfin forests, and least in upper elfin forests and in cloud forests. In contrast, regularity was greatest in lowland rainforest, dipping to its smallest values in mid-elevation cloud forests, and then increasing in high elevation elfin forests. These patterns indicate that the first species to drop out with increasing elevation are ones that are closely related to other species in the metacommunity. Measures of the effective number of phylogenetically independent or distinct species decreased very rapidly with elevation, and $\beta$-diversity was larger. In contrast, a comparison of feeding guilds shows a different effect of phylogenetic patterning. Along the elevational gradient, each guild generally loses some species from each clade–rather than entire clades–explaining the maintenance of functional diversity as phylogenetic diversity decreases.},
-author = {Scheiner, Samuel M. and Kosman, Evsey and Presley, Steven J. and Willig, Michael R.},
-doi = {10.1002/ece3.3199},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheiner et al. - 2017 - The components of biodiversity, with a particular focus on phylogenetic information.pdf:pdf},
-issn = {20457758},
-journal = {Ecology and Evolution},
-title = {{The components of biodiversity, with a particular focus on phylogenetic information}},
-url = {http://doi.wiley.com/10.1002/ece3.3199},
-volume = {in press},
-year = {2017}
-}
-@article{Surico2003,
-abstract = {Economic activities are highly clustered. Why is geographic concentration becoming a predominant feature of industrialized economies? On the basis of the empirical models developed by the new theories of international trade, our answer is that increasing returns are the driving force of economic geography in the US as well as in Europe. In so doing, we review several econometric methods proposed in the literature to separate and to test alternative theoretical paradigms.},
-author = {Surico, Paolo},
-doi = {10.1046/j.1467-6419.2003.00210.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Surico - 2003 - Geographic concentration and increasing returns.pdf:pdf},
-journal = {Journal of Economic Surveys},
-number = {5},
-pages = {693--708},
-title = {{Geographic concentration and increasing returns}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1467-6419.2003.00210.x/abstract},
-volume = {17},
-year = {2003}
-}
-@article{Hoffmann2008,
-abstract = {Jost [Jost, L., 2006. Entropy and diversity. Oikos, 113: 363–374.] recently discussed Hill's [Hill, M., 1973. Diversity and evenness: a unifying notation and its consequences. Ecology, 54: 427–431.] effective number of species and concluded by naming it the “true” diversity. In this note we comment on parts of Jost's work and argue that the true diversity is not what the name suggests.},
-author = {Hoffmann, S{\"{o}}nke and Hoffmann, Andreas},
-doi = {10.1016/j.ecolecon.2008.01.009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hoffmann, Hoffmann - 2008 - Is there a true diversity.pdf:pdf},
-journal = {Ecological Economics},
-number = {2},
-pages = {213--215},
-title = {{Is there a "true" diversity?}},
-url = {http://www.sciencedirect.com/science/article/pii/S0921800908000360},
-volume = {65},
-year = {2008}
-}
-@article{Munkemuller2012,
-abstract = {Ecological theory suggests that spatial distribution of biodiversity is strongly driven by community assembly processes. Thus the study of diversity patterns combined with null model testing has become increasingly common to infer assembly processes from observed distributions of diversity indices. However, results in both empirical and simulation studies are inconsistent. The aim of our study is to determine with simulated data which facets of biodiversity, if any, may unravel the processes driving its spatial patterns, and to provide practical considerations about the combination of diversity indices that would produce significant and congruent signals when using null models. The study is based on simulated species' assemblages that emerge under various landscape structures in a spatially explicit individual-based model with contrasting, predefined assembly processes. We focus on four assembly processes (species-sorting, mass effect, neutral dynamics and competition colonization trade-off) and investigate the emerging species' distributions with varied diversity indices (alpha, beta and gamma) measured at different spatial scales and for different diversity facets (taxonomic, functional and phylogenetic). We find that 1) the four assembly processes result in distinct spatial distributions of species under any landscape structure, 2) a broad range of diversity indices allows distinguishing between communities driven by different assembly processes, 3) null models provide congruent results only for a small fraction of diversity indices and 4) only a combination of these diversity indices allows identifying the correct assembly processes. Our study supports the inference of assembly processes from patterns of diversity only when different types of indices are combined. It highlights the need to combine phylogenetic, functional and taxonomic diversity indices at multiple spatial scales to effectively infer underlying assembly processes from diversity patterns by illustrating how combination of different indices might help disentangling the complex question of coexistence. {\textcopyright} 2011 The Authors. Journal compilation {\textcopyright} 2011 Nordic Society Oikos.},
-annote = {Cited By (since 1996):9
-Export Date: 23 October 2013
-Source: Scopus},
-author = {M{\"{u}}nkem{\"{u}}ller, Tamara and {De Bello}, Francesco and Meynard, Christine N. and Gravel, D. and Lavergne, S. and Mouillot, David and Mouquet, Nicolas and Thuiller, Wilfried},
-doi = {10.1111/j.1600-0587.2011.07259.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/M{\"{u}}nkem{\"{u}}ller et al. - 2012 - From diversity indices to community assembly processes A test with simulated data.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {468--480},
-title = {{From diversity indices to community assembly processes: A test with simulated data}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84860359238{\&}partnerID=40{\&}md5=81d83c92f27e13402adbd772e0aee30d},
-volume = {35},
-year = {2012}
-}
-@article{Guilhaumon2008,
-abstract = {Species-area relationships (SARs) are fundamental to the study of key and high-profile issues in conservation biology and are particularly widely used in establishing the broad patterns of biodiversity that underpin approaches to determining priority areas for biological conservation. Classically, the SAR has been argued in general to conform to a power-law relationship, and this form has been widely assumed in most applications in the field of conservation biology. Here, using nonlinear regressions within an information theoretical model selection framework, we included uncertainty regarding both model selection and parameter estimation in SAR modeling and conducted a global-scale analysis of the form of SARs for vascular plants and major vertebrate groups across 792 terrestrial ecoregions representing almost 97{\%} of Earth's inhabited land. The results revealed a high level of uncertainty in model selection across biomes and taxa, and that the power-law model is clearly the most appropriate in only a minority of cases. Incorporating this uncertainty into a hotspots analysis using multimodel SARs led to the identification of a dramatically different set of global richness hotspots than when the power-law SAR was assumed. Our findings suggest that the results of analyses that assume a power-law model may be at severe odds with real ecological patterns, raising significant concerns for conservation priority-setting schemes and biogeographical studies.},
-author = {Guilhaumon, Fran{\c{c}}ois and Gimenez, Olivier and Gaston, Kevin J and Mouillot, David},
-doi = {10.1073/pnas.0803610105},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guilhaumon et al. - 2008 - Taxonomic and regional uncertainty in species-area relationships and the identification of richness hotspots.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {40},
-pages = {15458--15463},
-title = {{Taxonomic and regional uncertainty in species-area relationships and the identification of richness hotspots}},
-url = {http://www.pnas.org/content/105/40/15458.abstract},
-volume = {105},
-year = {2008}
-}
-@article{Shorrocks2005,
-abstract = {This paper reviews the theory and application of the decomposition methods commonly used to measure the impact of spatial location on income inequality. It establishes some new theoretical results with potentially wide applicability, and examines empirical evidence drawn from a large number of countries.},
-author = {Shorrocks, Anthony and Wan, Guanghua},
-doi = {10.1093/jnlecg/lbh054},
-journal = {Journal of Economic Geography},
-number = {1},
-pages = {59--81},
-title = {{Spatial decomposition of inequality}},
-volume = {5},
-year = {2005}
-}
-@article{Sherwin2017,
-abstract = {Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q = 0), Shannon information (q = 1), and heterozygosity (q = 2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q = 2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance. Diversity of molecules or species is best summarised as a diversity profile. Such profiles are useful in studies spanning bioinformatics to physical landscapes. Shannon information is a neglected but particularly informative part of the profile. Shannon now has robust theoretical background for molecular ecology and evolution.},
-author = {Sherwin, W and Chao, Anne and Jost, Lou and Smouse, P.E.},
-doi = {10.1016/j.tree.2017.09.012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sherwin et al. - 2017 - Information Theory Broadens the Spectrum of Molecular Ecology and Evolution.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {12},
-pages = {948--963},
-title = {{Information Theory Broadens the Spectrum of Molecular Ecology and Evolution}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534717302550},
-volume = {32},
-year = {2017}
-}
-@article{Hanel2014,
-abstract = {The maximum entropy principle (MEP) is a method for obtaining the most likely distribution functions of observables from statistical systems by maximizing entropy under constraints. The MEP has found hundreds of applications in ergodic and Markovian systems in statistical mechanics, information theory, and statistics. For several decades there has been an ongoing controversy over whether the notion of the maximum entropy principle can be extended in a meaningful way to nonextensive, nonergodic, and complex statistical systems and processes. In this paper we start by reviewing how Boltzmann–Gibbs–Shannon entropy is related to multiplicities of independent random processes. We then show how the relaxation of independence naturally leads to the most general entropies that are compatible with the first three Shannon–Khinchin axioms, the -entropies. We demonstrate that the MEP is a perfectly consistent concept for nonergodic and complex statistical systems if their relative entropy can be factored into a generalized multiplicity and a constraint term. The problem of finding such a factorization reduces to finding an appropriate representation of relative entropy in a linear basis. In a particular example we show that path-dependent random processes with memory naturally require specific generalized entropies. The example is to our knowledge the first exact derivation of a generalized entropy from the microscopic properties of a path-dependent random process.},
-author = {Hanel, R. and Thurner, S. and Gell-Mann, M.},
-doi = {10.1073/pnas.1406071111},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hanel, Thurner, Gell-Mann - 2014 - How multiplicity determines entropy and the derivation of the maximum entropy principle for complex s.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences},
-number = {19},
-pages = {6905--6910},
-title = {{How multiplicity determines entropy and the derivation of the maximum entropy principle for complex systems}},
-url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1406071111},
-volume = {111},
-year = {2014}
-}
-@article{Rao1985,
-abstract = {A unified approach is given for constructing cross entropy and dissimilarity measures between probability distributions, based on a given entropy function or a diversity measure. Special properties of quadratic entropy introduced by Rao [7] are described. In particular it is shown that the square root of the Jensen difference (dissimilarity measure) arising out of a quadratic entropy provides a metric on a probability space. Several characterizations of quadratic entropy are obtained.},
-author = {Rao, C. Radhakrishna and Nayak, Tapan K.},
-doi = {10.1109/tit.1985.1057082},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rao, Nayak - 1985 - Cross entropy, dissimilarity measures, and characterizations of quadratic entropy.pdf:pdf},
-journal = {IEEE Transactions on Information Theory},
-number = {5},
-pages = {589--593},
-title = {{Cross entropy, dissimilarity measures, and characterizations of quadratic entropy}},
-volume = {31},
-year = {1985}
-}
-@article{Dice1945,
-author = {Dice, Lee R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dice - 1945 - Measures of the amount of ecologic association between species.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {297--302},
-title = {{Measures of the amount of ecologic association between species}},
-volume = {26},
-year = {1945}
-}
-@article{Yachi1999,
-abstract = {Although the effect of biodiversity on ecosystem functioning has become a major focus in ecology, its significance in a fluctuating environment is still poorly understood. According to the insurance hypothesis, biodiversity insures ecosystems against declines in their functioning because many species provide greater guarantees that some will maintain functioning even if others fail. Here we examine this hypothesis theoretically. We develop a general stochastic dynamic model to assess the effects of species richness on the expected temporal mean and variance of ecosystem processes such as productivity, based on individual species' productivity responses to environmental fluctuations. Our model shows two major insurance effects of species richness on ecosystem productivity: (i) a buffering effect, i.e., a reduction in the temporal variance of productivity, and (ii) a performance-enhancing effect, i.e., an increase in the temporal mean of productivity. The strength of these insurance effects is determined by three factors: (i) the way ecosystem productivity is determined by individual species responses to environmental fluctuations, (ii) the degree of asynchronicity of these responses, and (iii) the detailed form of these responses. In particular, the greater the variance of the species responses, the lower the species richness at which the temporal mean of the ecosystem process saturates and the ecosystem becomes redundant. These results provide a strong theoretical foundation for the insurance hypothesis, which proves to be a fundamental principle for understanding the long-term effects of biodiversity on ecosystem processes.},
-author = {Yachi, Shigeo and Loreau, Michel},
-doi = {10.1073/pnas.96.4.1463},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yachi, Loreau - 1999 - Biodiversity and ecosystem productivity in a fluctuating environment the insurance hypothesis.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {4},
-pages = {1463--1468},
-title = {{Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis.}},
-url = {http://www.pnas.org/content/96/4/1463},
-volume = {96},
-year = {1999}
-}
-@article{Griffith1996,
-abstract = {Gaining a better understanding of spatial data and a deeper meaning of spatial statistical results gleaned from geo-referneced data requires a more complete knowledge of properties of the underlying geometry. These topics are addressed by further investigating important geometric features of spatial data.},
-author = {Griffith, Daniel A.},
-doi = {10.1111/j.1541-0064.1996.tb00462.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Griffith - 1996 - Spatial autocorrelation and eigenfunctions of the geographic weights matrix accompanying geo-referenced data.pdf:pdf},
-journal = {Canadian Geographer},
-number = {4},
-pages = {351--367},
-title = {{Spatial autocorrelation and eigenfunctions of the geographic weights matrix accompanying geo-referenced data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0064.1996.tb00462.x/abstract},
-volume = {40},
-year = {1996}
-}
-@article{Wolda1983,
-abstract = {Fluctuation patterns of insect species in the humid tropics are compared with those from the temperate zone, using data on species abundance covering a period of at least 6 years. The stability of a set of species is characterized by a Stability Index, which is, basically, the mean of the variances of the abundances of these species. Data on Homoptera, Dictyoptera, Orthoptera and mosquitos from the Panama Canal Area are compared with information from Europe, Australia and Japan. It is concluded that these tropical insects, even the ones from a relatively undisturbed tropical forest, are just as variable, or stable, as these temperate ones. Some exceptional temperate haibtats, such as the Schreierbach in Austria, seem to be much more stable than any known tropical ones.},
-author = {Wolda, Henk},
-doi = {10.1007/BF02539633},
-isbn = {0034-5466},
-issn = {00345466},
-journal = {Researches on Population Ecology},
-number = {3 Supplement},
-pages = {112--126},
-title = {{"Long-term" stability of tropical insect populations}},
-volume = {25},
-year = {1983}
-}
-@article{Botta-Dukat2005,
-abstract = {Question: Is Rao's quadratic entropy a suitable measure of functional diversity if several traits are considered? Methods: It is checked whether Rao's quadratic entropy (FDQ) satisfies a priori criteria suggested by Mason et al. A real data set is used to show that there are often zeros in abundance distributions which maximize functional diversity. Results and Conclusion: FDQ fulfils all a priori criteria and it surpasses other proposed indices, because it includes species abundances and more than one trait. Therefore, it seems to be an improvement compared to measures of functional diversity that are currently available. An unexpected property of FDQ is that its value may decrease if species richness increases. The reason is that functional diversity is influenced by both species- abundance based diversity and differences among species. Introduction of a new species into the community increases the species-abundance based diversity, while it may decrease the average dissimilarity among species.},
-author = {Botta-Duk{\'{a}}t, Zolt{\'{a}}n},
-doi = {10.1111/j.1654-1103.2005.tb02393.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Botta-Duk{\'{a}}t - 2005 - Rao's quadratic entropy as a measure of functional diversity based on multiple traits.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {533--540},
-title = {{Rao's quadratic entropy as a measure of functional diversity based on multiple traits}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2005.tb02393.x/abstract},
-volume = {16},
-year = {2005}
-}
-@article{Scheiner2012,
-abstract = {A metric of biodiversity is proposed that combines three of its key components: abundance, phylogeny, and ecological function. This metric is an expansion of the current abundance-based metric that uses Hill numbers, the effective number of types in a sample if all types had the same mean proportional abundance. I define analogous proportional measures of phylogenetic divergence and functional distinctiveness. Phylogenetic divergence is measured as the sum of the proportional share of each species of a given branch of a phylogeny. Functional distinctiveness can be measured in two ways, as the proportional share of each species of a specified ecological function, or as the relative distance of each species based on functional trait values. Because all three aspects of biodiversity are measured in the same fashion (relative proportions) in similar units (effective numbers of species), an integrated metric can be defined. The combined metric provides understanding of covariation among the components and how management for one component may trade off against others. The metric can be partitioned into components of richness and evenness, and into subsets and variation among subsets, all of which can be related through a simple multiplicative framework. This metric is a complement to, rather than a replacement of, current metrics of phylogenetic and functional diversity. More work is needed to link this new metric to ecological theory, determine its error structure, and devise methods for its effective assessment.},
-author = {Scheiner, Samuel M.},
-doi = {10.1111/j.1600-0706.2012.20607.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheiner - 2012 - A metric of biodiversity that integrates abundance, phylogeny, and function.pdf:pdf},
-journal = {Oikos},
-number = {8},
-pages = {1191--1202},
-title = {{A metric of biodiversity that integrates abundance, phylogeny, and function}},
-url = {http://dx.doi.org/10.1111/j.1600-0706.2012.20607.x},
-volume = {121},
-year = {2012}
-}
-@article{Appleby1996,
-abstract = {The generalized entropy, calculated from the quadrat counts of the population of the United States and Great Britain, is plotted against the logarithm of the quadrat size. These graphs are linear over a range of scales that corresponds to the size of a city up to the size of the country. This linearity indicates a strong scale-invariant component to the spatial population distribution pattern. Measurements of the generalized q-dimensions and alpha spectrum of the spatial population distribution patterns estimated from these graphs are presented.},
-author = {Appleby, Stephen},
-doi = {10.1111/j.1538-4632.1996.tb00926.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Appleby - 1996 - Multifractal Characterization of the Distribution Pattern of the Human Population.pdf:pdf},
-journal = {Geographical Analysis},
-number = {2},
-pages = {147--160},
-title = {{Multifractal Characterization of the Distribution Pattern of the Human Population}},
-url = {http://doi.wiley.com/10.1111/j.1538-4632.1996.tb00926.x},
-volume = {28},
-year = {1996}
-}
-@article{Gemerden2003,
-abstract = {Aim Tropical rain forests are often regarded as pristine and undisturbed by humans. In Central Africa, community-wide disturbances by natural causes are rare and therefore current theory predicts that natural gap phase dynamics structure tree species composition and diversity. However, the dominant tree species in many African forests recruit poorly, despite the presence of gaps. To explain this, we studied the disturbance history of a species-rich and structurally complex rain forest. Location Lowland rain forest in Southern Cameroon. Methods We identified the recruitment conditions of trees in different diameter classes in 16 ha of species-rich and structurally complex ‘old growth' rain forest. For the identification of recruitment preference we used independent data on the species composition along a disturbance gradient, ranging from shifting cultivation fields (representing large-scale disturbance), to canopy gaps and old growth forest. Results In nine of sixteen 1-ha forest plots the older trees preferred shifting cultivation fields for recruitment while younger trees preferred gaps and closed forest conditions. This indicates that these nine sites once experienced large-scale disturbances. Three lines of evidence suggest that historical agricultural use is the most likely disturbance factor: (1) size of disturbed and undisturbed patches, (2) distribution of charcoal and (3) historical accounts of human population densities. Main conclusions Present-day tree species composition of a structurally complex and species-rich Central African rain forest still echoes historical disturbances, most probably caused by human land use between three to four centuries ago. Human impact on African rain forest is therefore, contrary to common belief, an issue not of the last decades only. Insights in historical use will help to get a more balanced view of the ‘pristine rain forest', acknowledging that the dualism between ‘old growth' and ‘secondary' forest may be less clear than previously thought.},
-author = {van Gemerden, Barend S. and Olff, Han and Parren, Marc P.E. and Bongers, Frans},
-doi = {10.1046/j.1365-2699.2003.00937.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/van Gemerden et al. - 2003 - The pristine rain forest Remnants of historical human impacts on current tree species composition and diver.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {9},
-pages = {1381--1390},
-title = {{The pristine rain forest? Remnants of historical human impacts on current tree species composition and diversity}},
-url = {http://doi.wiley.com/10.1046/j.1365-2699.2003.00937.x},
-volume = {30},
-year = {2003}
-}
-@article{Pelissier2007,
-abstract = {An important goal of community ecology is the assessment of factors that are likely to influence the spatio-temporal distribution of species assemblages and diversity. Surprisingly, most statistical methods devoted to this have remained poorly interconnected, as well as poorly connected with the popular metrics of diversity estimation. In the present paper we show that important questions related to determinants of species diversity can be specified through a simple multivariate linear model and explored, in common diversity metrics, using standard methods and routines of variance/covariance decomposition. Thanks to an unusual form of presentation of taxonomic data into a table of species occurrences, which considers the individuals as data units, Shannon and Simpson indices as well as species richness can all be expressed as a (weighted) sum of squares. Subsequent apportionments into explained and residual sum of squares provide direct estimates of the beta- and alpha-diversity components with respect to either categorical habitat types or continuous gradient variables. Appropriate statistics and non-parametric tests are available to assess the significance of these components. Explicit analytical relationships exist between the linear approximation of the table of species occurrences by sampling sites, and the more classical table of species abundances by sites. Therefore, direct links with methods of ordination in reduced space, such as correspondence analysis and canonical correspondence analysis, provide opportunities for partitions that preserve consistency with usual diversity indices. The sum of squares of the approximated occurrence table provides measures of intersites beta-diversity, from which measures of dissimilarity with explicit references to diversity indices can be derived. Such measures are amenable to distance-based apportionments through multivariate variograms and multiscale ordination. What are the relative effects of the biological, environmental and anthropogenic factors and of their potential interactions on species diversity? Are these effects stable across scales, from landscape to region, between regions and across ecosystems? The methodological integration proposed in our analytical framework enables one to address these questions using standard statistical tools, and opens new prospects for quantitative biodiversity studies. This also paves the way towards refined models for predicting species diversity at unsampled locations.},
-annote = {Pelissier, Raphael Couteron, Pierre},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l and Couteron, Pierre},
-doi = {10.1111/j.1365-2745.2007.01211.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/P{\'{e}}lissier, Couteron - 2007 - An operational, additive framework for species diversity partitioning and beta-diversity analysis.pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {294--300},
-title = {{An operational, additive framework for species diversity partitioning and beta-diversity analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2007.01211.x/abstract},
-volume = {95},
-year = {2007}
-}
-@article{Chalmandrier2014a,
-abstract = {Different assembly processes drive the spatial structure of meta-communities ($\beta$-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high $\beta$-diversity along environmental gradients should be the result of environmental filtering while low $\beta$-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting $\beta$-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf–height–seed spectrum) and phylogenetic facets of $\beta$-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional $\beta$-diversity was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic $\beta$-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species' dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.},
-author = {Chalmandrier, Lo{\"{i}}c and M{\"{u}}nkem{\"{u}}ller, Tamara and Lavergne, S{\'{e}}bastien and Thuiller, Wilfried},
-doi = {10.1890/13-2153.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chalmandrier et al. - 2014 - Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant met(2).pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {143--153},
-title = {{Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community}},
-url = {http://www.esajournals.org/doi/abs/10.1890/13-2153.1},
-volume = {96},
-year = {2014}
-}
-@article{Pielou1972,
-abstract = {Suppose r different animal species are found in some or all of c different habitats. Observations on the numbers of occurrences of the animals in the habitats can be tabulated in an r X c table. The overall "diversity" of the table, HT say, is defined as Brillouin's infor- mation measure with the r X c table's cell frequencies as the frequencies of the different "symbols." It is shown that HT may be split into two components in two different ways. The first way splits HT into HA, the diversity of the animal species, plus the weighted mean of the within-species habitat diversities. The second way splits HT into HB' the diversity of the hab- itats, plus the weighted mean of the within-habitat species diversities. The weighted mean of within-species habitat diversities constitutes a measure of the average niche width of the r species of animals. The weighted mean of within-habitat species diversities constitutes a measure of the average niche overlap among the c habitats examined. The measures are of actual, realized niche widths and niche overlaps and are therefore inevitably affected by the relative abundances of the species and the habitats. A method of standardizing them is proposed. An example is given using data on the occurrences of several species of aphids on several host plants of the genus Solidago (goldenrods).},
-author = {Pielou, Evelyn C.},
-doi = {10.2307/1934784},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1972 - Niche width and niche overlap a method for measuring them.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {687--692},
-title = {{Niche width and niche overlap: a method for measuring them}},
-volume = {53},
-year = {1972}
-}
-@article{Decrouez2016,
-abstract = {For a probability distribution Ρ on an at most countable alphabet {\$}\backslashmathcal A{\$}, this article gives finite sample bounds for the expected occupancy counts {\$}\backslashmathbb E K{\_}{\{}n,r{\}}{\$} and probabilities {\$}\backslashmathbb E M{\_}{\{}n,r{\}}{\$}. In particular, both upper and lower bounds are given in terms of the right tail $\nu$ of the counting measure of Ρ. Special attention is given to the case where $\nu$ is bounded by a regularly varying function. In this case, it is shown that our general results lead to an optimal-rate control of the expected occupancy counts and probabilities with explicit constants. Our results are also put in perspective with Turing's formula and recent concentration bounds to deduce confidence regions. At the end of the paper, we discuss an extension of the occupancy problem to arbitrary distributions in a metric space.},
-archivePrefix = {arXiv},
-arxivId = {1601.06537},
-author = {Decrouez, Geoffrey and Grabchak, Michael and Paris, Quentin},
-eprint = {1601.06537},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Decrouez, Grabchak, Paris - 2016 - Finite sample properties of the mean occupancy counts and probabilities.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Finite sample properties of the mean occupancy counts and probabilities}},
-url = {http://arxiv.org/abs/1601.06537v1 papers2://publication/uuid/4C6EFA69-E6B3-44FC-965B-64240BB0A560},
-volume = {1601.06537},
-year = {2016}
-}
-@article{Chave2002a,
-abstract = {Mechanisms proposed to explain the maintenance of species diversity within ecological communities of sessile organisms include niche differentiation mediated by competitive trade-offs, frequency dependence resulting from species-specific pests, recruitment limitation due to local dispersal, and a speciation-extinction dynamic equilibrium mediated by stochasticity (drift). While each of these processes, and more, have been shown to act in particular communities, much remains to be learned about their relative importance in shaping community-level patterns. We used a spatially-explicit, individual-based model to assess the effects of each of these processes on species richness, relative abundance, and spatial patterns such as the species-area curve. Our model communities had an order-of-magnitude more individuals than any previous such study, and we also developed a finite-size scaling analysis to infer the large-scale properties of these systems in order to establish the generality of our conclusions across system sizes. As expected, each mechanism can promote diversity. We found some qualitative differences in community patterns across communities in which different combinations of these mechanisms operate. Species-area curves follow a power law with short-range dispersal and a logarithmic law with global dispersal. Relative-abundance distributions are more even for systems with competitive differences and trade-offs than for those in which all species are competitively equivalent, and they are most even when frequency dependence (even if weak) is present. Overall, however, communities in which different processes operated showed surprisingly similar patterns, which suggests that the form of community-level patterns cannot in general be used to distinguish among mechanisms maintaining diversity there. Nevertheless, parameterization of models such as these from field data on the strengths of the different mechanisms could yield insight into their relative roles in diversity maintenance in any given community.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Muller-Landau, Helene C. and Levin, Simon A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Muller-Landau, Levin - 2002 - Comparing classical community models theoretical consequences for patterns of diversity.pdf:pdf},
-journal = {The American Naturalist},
-number = {1},
-pages = {1--23},
-title = {{Comparing classical community models: theoretical consequences for patterns of diversity}},
-url = {http://www.jstor.org/stable/10.1086/324112},
-volume = {159},
-year = {2002}
-}
-@article{Haase1995,
-abstract = {Spatial pattern analysis based on Ripley´s K-function is a second-order analysis of point patterns in a two-dimensional space. The method is increasingly used in studies of spatial distribution patterns of plant communities, but the statistical methods involved are sometimes poorly understood or have been modified without evaluating the effects on results. The procedures of field data acquisition, statistical analysis, and the test for the null hypothesis of complete spatial randomness are described and the presentation of results is discussed. Different methods of edge correction were tested on a computer-generated random pattern and a mapped distribution of a Mediterranean shrubland. The inclusion of buffer zones around mapped plots describes the spatial pattern most accurately, but may not warrant the additional labour involved. Three variations of the weighted edge correction yielded comparable results for the distribution patterns tested. The toroidal edge correction may give biased results for non-random patterns. Recommendations for standardisation of the statistical procedures and data presentation are given .},
-author = {Haase, Peter},
-doi = {10.2307/3236356},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haase - 1995 - Spatial pattern analysis in ecology based on Ripley's K function Introduction and methods of edge correction.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {575--582},
-title = {{Spatial pattern analysis in ecology based on Ripley's K function: Introduction and methods of edge correction}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236356/abstract},
-volume = {6},
-year = {1995}
-}
-@book{Fujita1999,
-address = {Cambridge},
-author = {Fujita, Masahisa and Krugman, Paul and Venables, Anthony J},
-publisher = {The MIT Press},
-title = {{The Spatial Economy}},
-year = {1999}
-}
-@article{Kim1999,
-abstract = {This paper estimates the Rybczynski equation matrix for the twenty two-digit U.S. manufacturing industries for various years between 1880 and 1987. As predicted by the standard general equilibrium theory of interregional trade, the regression estimates show that a consistent set of factor endowments explains a significant amount of the geographic distribution of manufacturing activities over time. Although these results do not rule out the importance of increasing returns, they do suggest certain limits on how increasing returns affect U.S. economic geography.},
-author = {Kim, Sukkoo},
-doi = {10.1016/S0166-0462(98)00010-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kim - 1999 - Regions, resources, and economic geography Sources of U.S. regional comparative advantage, 1880-1987.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {1},
-pages = {1--32},
-title = {{Regions, resources, and economic geography: Sources of U.S. regional comparative advantage, 1880-1987}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046298000106},
-volume = {29},
-year = {1999}
-}
-@article{Ricotta2003a,
-abstract = {A measure of beta-diversity based on the distribution of Kullback's information-theoretical divergence of single plots from the pooled sample is proposed for data on species relative abundances. Unlike other indices explicitly developed to summarise plot-to-plot variability along an environmental gradient, the proposed measure provides meaningful estimates of {\^{I}}²-diversity independently of the presence of coenoclines. In the present study, a classical artificial data set is used to illustrate its application. Further, some analogies between the proposed measure and Whittaker's index of beta-diversity are discussed.},
-author = {Ricotta, Carlo and Avena, Giancarlo C.},
-doi = {10.1080/11263500312331351331},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Avena - 2003 - An information-theoretical measure of beta-diversity.pdf:pdf},
-journal = {Plant Biosystems},
-number = {1},
-pages = {57--61},
-title = {{An information-theoretical measure of beta-diversity}},
-url = {http://www.informaworld.com/10.1080/11263500312331351331},
-volume = {137},
-year = {2003}
-}
-@article{Marshall1991,
-abstract = {A review of methods for the analysis of the geographical distribution of disease is presented. The topic is of increasing interest to statisticians, though much groundwork has been done by epidemiologists and medical geographers. Methods for the detection and testing for apparent clusters of disease, including those near a possible environmental hazard, are reviewed. Estimating regional mortality rates, possibly to construct disease maps, and methods for investigating the association between disease rates and social, demographic and environmental factors are discussed. In addition, statistical analysis of the spatial spread of epidemics is mentioned.},
-author = {Marshall, Roger J.},
-doi = {10.2307/2983152},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marshall - 1991 - A Review of Methods for the Statistical Analysis of Spatial Patterns of Disease.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {3},
-pages = {421--441},
-title = {{A Review of Methods for the Statistical Analysis of Spatial Patterns of Disease}},
-volume = {154},
-year = {1991}
-}
-@article{Yang2012,
-abstract = {This paper describes a simulation model of the spatial development of economic activities over time. The key principle addressed is how spatial patterns of economic activity emerge from decisions of individual firms, which are in turn influenced by the existing spatial configuration. A stylized simulation is presented, in which two types of firms grow at different rates, giving rise to split offs and spatial relocations. The influence of the spatial pattern on individual firms' decisions is implemented in various ways, related to well-known effects such as Jacobs and Marshall externalities described in the economic literature and congestion effects. We demonstrate that different assumptions about the spatial scale of these externalities lead to different spatial configurations. Function concentration (Marshall effects) is more likely to lead to the emergence of subcentres with a specific specialisation. However, the spatial scale of the market and agglomeration effects matters. In particular, if Marshall advantages stretch out over a longer distance, more subcentres emerge. Somewhat surprisingly, congestion seems to have a minor impact on the emerging patterns. The simulation outcomes are intuitively plausible, suggesting that micro-simulation is a promising tool for developing forecasting models to support spatial and economic policies. However, they also articulate the need for validation of the behavioural decision rules, in particular by investigating how growth rates and the spatial scale of externalities differs between different industrial sectors. {\textcopyright} JASSS.},
-annote = {Export Date: 25 January 2013
-Source: Scopus},
-author = {Yang, Jung-Hun and Ettema, Dick},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yang, Ettema - 2012 - Modelling the emergence of spatial patterns of economic activity.pdf:pdf},
-journal = {Journal of Artificial Societies and Social Simulation},
-number = {4},
-title = {{Modelling the emergence of spatial patterns of economic activity}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84868530803{\&}partnerID=40{\&}md5=103f6ea9a5666ebd1d19239caaa703e3},
-volume = {15},
-year = {2012}
-}
-@unpublished{Loiret2013,
-author = {Loiret, Richard},
-booktitle = {REEDS Working Papers},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loiret - 2013 - L'indice Ka de distance {\`{a}} l'{\'{e}}quilibre et la diversit{\'{e}} biologique.pdf:pdf},
-title = {{L'indice Ka de distance {\`{a}} l'{\'{e}}quilibre et la diversit{\'{e}} biologique}},
-volume = {2013-04},
-year = {2013}
-}
-@book{Ehrlich1981,
-address = {New York},
-annote = {Th{\'{e}}orie des rivets.},
-author = {Ehrlich, Paul R. and Ehrlich, Anne H.},
-publisher = {Random House},
-title = {{Extinction: The Causes vand Consequences of the disappearance of Species}},
-year = {1981}
-}
-@article{Gregorius1991,
-abstract = {A generalized conceptual basis for Wright's notion of effective size is presented. The concept is applied to the calculation of effective numbers based on the rate of change of genetic variability. With particular reference to the inbreeding, the eigen value, and the newly introduced "diversity" effective size, the use of the concept as a means for discrimination between and identification of various effective sizes is demonstrated.},
-author = {Gregorius, Hans-Rolf},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 1991 - On the concept of effective number.pdf:pdf},
-journal = {Theoretical population biology},
-number = {2},
-pages = {269--83},
-title = {{On the concept of effective number}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/1788824},
-volume = {40},
-year = {1991}
-}
-@article{Mao2007,
-abstract = {Diversity arises as a significant concept in many scientific fields, and particularly in ecology. The relationships between diversity indices and species accumulation functions are investigated. Nonparametric methods are illustrated with ecological examples.},
-author = {Mao, Chang Xuan},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mao - 2007 - Estimating Species Accumulation Curves and Diversity Indices.pdf:pdf},
-journal = {Statistica Sinica},
-pages = {761--774},
-title = {{Estimating Species Accumulation Curves and Diversity Indices}},
-volume = {17},
-year = {2007}
-}
-@article{Leinster2015,
-abstract = {Entropy, under a variety of names, has long been used as a measure of diversity in ecology, as well as in genetics, economics and other fields. There is a spectrum of viewpoints on diversity, indexed by a real parameter q giving greater or lesser importance to rare species. Leinster and Cobbold (2012) proposed a one-parameter family of diversity measures taking into account both this variation and the varying similarities between species. Because of this latter feature, diversity is not maximized by the uniform distribution on species. So it is natural to ask: which distributions maximize diversity, and what is its maximum value? In principle, both answers depend on q, but our main theorem is that neither does. Thus, there is a single distribution that maximizes diversity from all viewpoints simultaneously, and any list of species has an unambiguous maximum diversity value. Furthermore, the maximizing distribution(s) can be computed in finite time, and any distribution maximizing diversity from some particular viewpoint q {\textgreater} 0 actually maximizes diversity for all q. Although we phrase our results in ecological terms, they apply very widely, with applications in graph theory and metric geometry.},
-archivePrefix = {arXiv},
-arxivId = {1512.06314},
-author = {Leinster, Tom and Meckes, Mark W.},
-doi = {10.3390/e18030088},
-eprint = {1512.06314},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leinster, Meckes - 2016 - Maximizing diversity in biology and beyond(2).pdf:pdf},
-journal = {Entropy},
-number = {3},
-pages = {88},
-title = {{Maximizing diversity in biology and beyond}},
-url = {http://www.mdpi.com/1099-4300/18/3/88},
-volume = {18},
-year = {2016}
-}
-@article{Szwagrzyk1993,
-abstract = {The analysis of spatial patterns is one of the ways to estimate the role of competition among trees in forest dynamics. Three hypotheses concerning distribution patterns in old-growth stands were tested: (1) fine-scale spatial patterns of trees are regular; (2) patterns do not differ significantly from a random distribution, and (3) spatial patterns at larger scales are clumped because of site heterogeneity. Old-growth forest stands in Poland and the Czech Republic were analysed with a modified Ripley K function, using distribution maps of tree stems. Fine-scale spatial patterns (with distances among trees not exceeding 15 m) were usually intermediate between random and regular. Trends towards a regular distribution occurred more often among dead than among live individuals. No significant relationships between tree species were found at smaller scales; however, at larger scales (distances from 15–25 m) negative associations between some species were found. This reflects site heterogeneity rather than any direct influence of one tree species upon another.},
-author = {Szwagrzyk, Jerzy and Czerwczak, Marek},
-doi = {10.2307/3236074},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Szwagrzyk, Czerwczak - 1993 - Spatial patterns of trees in natural forests of East-Central Europe.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {469--476},
-title = {{Spatial patterns of trees in natural forests of East-Central Europe}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236074/abstract},
-volume = {4},
-year = {1993}
-}
-@article{May2016a,
-abstract = {Aim: It has been recently suggested that different 'unified theories of biodiversity and biogeography' can be characterized by three common 'minimal sufficient rules': (1) species abundance distributions follow a hollow curve, (2) species show intraspecific aggregation, and (3) species are independently placed with respect to other species. Here, we translate these qualitative rules into a quantitative framework and assess if these minimal rules are indeed sufficient to predict multiple macroecological biodiversity patterns simultaneously. Location: Tropical forest plots in Barro Colorado Island (BCI), Panama, and in Sinharaja, Sri Lanka. Methods: We assess the predictive power of the three rules using dynamic and spatial simulation models in combination with census data from the two forest plots. We use two different versions of the model: (1) a neutral model and (2) an extended model that allowed for species differences in dispersal distances. In a first step we derive model parameterizations that correctly represent the three minimal rules (i.e. the model quantitatively matches the observed species abundance distribution and the distribution of intraspecific aggregation). In a second step we applied the parameterized models to predict four additional spatial biodiversity patterns. Results: Species-specific dispersal was needed to quantitatively fulfil the three minimal rules. The model with species-specific dispersal correctly predicted the species-area relationship, but failed to predict the distance decay, the relationship between species abundances and aggregations, and the distribution of a spatial co-occurrence index of all abundant species pairs. These results were consistent over the two forest plots. Main conclusions: The three 'minimal sufficient' rules only provide an incomplete approximation of the stochastic spatial geometry of biodiversity in tropical forests. The assumption of independent interspecific placements is most likely violated in many forests due to shared or distinct habitat preferences. Furthermore, our results highlight missing knowledge about the relationship between species abundances and their aggregation.},
-author = {May, Felix and Wiegand, Thorsten and Lehmann, Sebastian and Huth, Andreas},
-doi = {10.1111/geb.12438},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May et al. - 2016 - Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tro(2).pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {5},
-pages = {575--585},
-title = {{Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tropical forests?}},
-url = {http://doi.wiley.com/10.1111/geb.12438},
-volume = {25},
-year = {2016}
-}
-@article{Ricotta2006b,
-abstract = {The diversity of a species assemblage has been studied extensively for many decades in relation to its possible connection with ecosystem functioning and organization. In this view most diversity measures, such as Shannon's entropy, rely upon information theory as a basis for the quantification of diversity. Also, traditional diversity measures are computed using species relative abundances and cannot account for the ecological differences between species. Rao first proposed a diversity index, termed quadratic diversity (Q) that incorporates both species relative abundances and pairwise distances between species. Quadratic diversity is traditionally defined as the expected distance between two randomly selected individuals. In this paper, we show that quadratic diversity can be interpreted as the expected conflict among the species of a given assemblage. From this unusual interpretation, it naturally follows that Rao's Q can be related to the Shannon entropy through a generalized version of the Tsallis parametric entropy.},
-author = {Ricotta, Carlo and Szeidl, Laszlo},
-doi = {10.1016/j.tpb.2006.06.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Szeidl - 2006 - Towards a unifying approach to diversity measures Bridging the gap between the Shannon entropy and Rao's quadra.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {3},
-pages = {237--243},
-title = {{Towards a unifying approach to diversity measures: Bridging the gap between the Shannon entropy and Rao's quadratic index}},
-url = {http://www.sciencedirect.com/science/article/pii/S004058090600075X},
-volume = {70},
-year = {2006}
-}
-@article{Good1953,
-abstract = {A random sample is drawn from a population of animals of various species. (The theory may also be applied to studies of literary vocabulary, for example.) If a particular species is represented r times in the sample of size N, then r/N is not a good estimate of the population frequency, p, when r is small. Methods are given for estimating p, assuming virtually nothing about the underlying population. The estimates are expressed in terms of smoothed values of the numbers nr (r= 1, 2, 3, ...), where nr is the number of distinct species that are each represented r times in the sample. (nr may be described as ‘the frequency of the frequency r'.) Turing is acknowledged for the most interesting formula in this part of the work. An estimate of the proportion of the population represented by the species occurring in the sample is an immediate corollary. Estimates are made of measures of heterogeneity of the population, including Yule's ‘characteristic' and Shannon's ‘entropy'. Methods are then discussed that do depend on assumptions about the underlying population. It is here that most work has been done by other writers. It is pointed out that a hypothesis can give a good fit to the numbers nr but can give quite the wrong value for Yule's characteristic. An example of this is Fisher's fit to some data of Williams's on Macrolepidoptera.},
-author = {Good, I. J.},
-doi = {10.1093/biomet/40.3-4.237},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Good - 1953 - The Population Frequency of Species and the Estimation of Population Parameters.pdf:pdf},
-journal = {Biometrika},
-number = {3/4},
-pages = {237--264},
-title = {{The Population Frequency of Species and the Estimation of Population Parameters}},
-volume = {40},
-year = {1953}
-}
-@article{Maire2015,
-abstract = {Functional diversity is a key facet of biodiversity that is increasingly being measured to quantify its changes following disturbance and to understand its effects on ecosystem functioning. Assessing the functional diversity of assemblages based on species traits requires the building of a functional space (dendrogram or multidimensional space) where indices will be computed.However, there is still no consensus on the best method for measuring the quality of functional spaces. Innovation Here we propose a framework for evaluating the quality of a func- tional space (i.e. the extent to which it is a faithful representation of the initial functional trait values). Using simulated datasets, we analysed the influence of the number and type of functional traits used and of the number of species studied on the identity and quality of the best functional space. We also tested whether the quality of the functional space affects functional diversity patterns in local assem- blages, using simulated datasets and a real study case. Main conclusions The quality of functional space strongly varied between situa- tions. Spaces having at least four dimensions had the highest quality, while func- tional dendrograms and two-dimensional functional spaces always had a low quality. Importantly, we showed that using a poor-quality functional space could led to a biased assessment of functional diversity and false ecological conclusions. Therefore,we advise a pragmatic approach consisting of computing all the possible functional spaces and selecting the most parsimonious one.},
-author = {Maire, Eva and Grenouillet, Ga{\"{e}}l and Brosse, S{\'{e}}bastien and Vill{\'{e}}ger, S{\'{e}}bastien},
-doi = {10.1111/geb.12299},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Maire et al. - 2015 - How many dimensions are needed to accurately assess functional diversity A pragmatic approach for assessing the qu.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {6},
-pages = {728--740},
-title = {{How many dimensions are needed to accurately assess functional diversity? A pragmatic approach for assessing the quality of functional spaces}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12299/abstract},
-volume = {24},
-year = {2015}
-}
-@article{Novotny2002,
-abstract = {Predictability in the composition of tropical assemblages of insect herbivores was studied using a sample of 35,952 caterpillars (Lepidoptera) from 534 species, feeding on 69 woody species from 45 genera and 23 families in a lowland rainforest in Papua New Guinea. Caterpillar assemblages were strongly dominated by a single species (median 48{\%} of individuals and 49{\%} of biomass). They were spatially and temporally constant (median normalized expected species shared (NESS) similarity between assemblages from the same host was greater than or equal to 0.85 for three sites 8-17 km apart as well as for three four-month periods of the year). Further, the median presence of species was 11 months per year. Assemblages on hosts from different families and genera were virtually disjunct (NESS similarity less than 0.05) as the caterpillars were mostly specialized to a single plant family (77{\%} of species) and, within families, to a single genus (66{\%} of species), while capable of feeding on multiple congeneric hosts (89{\%} of species). The dominance of caterpillar assemblages by a small number of specialized species, which also exhibited low spatial and temporal variability, permitted robust and reliable estimates of assemblage composition and between-assemblage similarity from small samples, typically less than 300 individuals per host plant. By contrast, even considerably larger samples were insufficient for estimates of species richness. A sample of 300 individuals was typically obtained from 1,050 m(2) of foliage sampled during 596 tree inspections (i.e. a particular tree sampled at a particular time) in the course of 19 sampling days (median values from 69 assemblages). These results demonstrate that, contrary to some previous suggestions, insect herbivore assemblages in tropical rainforests have a predictable structure and, as such, are amenable to study.},
-author = {Novotny, V. and Miller, S. E. and Basset, Y. and Cizek, L. and Drozd, P. and Darrow, K. and Leps, J.},
-doi = {10.1098/rspb.2002.2166},
-isbn = {0962-8452},
-issn = {0962-8452},
-journal = {Proceedings of the Royal Society B: Biological Sciences},
-number = {1507},
-pages = {2337--2344},
-pmid = {12495501},
-title = {{Predictably simple: assemblages of caterpillars (Lepidoptera) feeding on rainforest trees in Papua New Guinea}},
-url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2002.2166},
-volume = {269},
-year = {2002}
-}
-@article{Haffer1997,
-abstract = {The main hypotheses proposed to explain barrier formation separating populations and causing the differentiation of vertebrate species in Amazonia are based on different (mostly historical) factors, as follows. (1) Changes in the distribution of land and sea or in the landscape due to tectonic movements or sea-level fluctuations (Paleogeography hypothesis). (2) The barrier effect of Amazonian rivers (River hypothesis). (3) A combination of the barrier effect of broad rivers and vegetational changes in Northern and Southern Amazonia (River-refuge hypothesis). (4) The isolation of forest blocks near areas of surface relief in the periphery of Amazonia during dry climatic periods of the Tertiary and Quaternary (Refuge theory). (5) Competitive species interactions and local species isolations in peripheral regions of Amazonia due to invasion and counterinvasion during cold/warm periods of the Pleistocene (Disturbance-vicariance hypothesis). (6) Parapatric speciation across steep environmental gradients without separation of the representative populations (Gradient hypothesis). Several of these hypotheses are probably relevant to a different degree for the speciation processes in different faunal groups or during different geological periods. The paleogeography hypothesis refers mainly to faunal differentiation during the Tertiary and in combination with the Refuge hypothesis; Milankovitch cycles leading to global climatic-vegetational changes affected the biomes of the world not only during the Pleistocene but also during the Tertiary and earlier geological periods. New geoscientific evidence for the effect of dry climatic periods in Amazonia supports the predictions of the Refuge theory},
-author = {Haffer, Jurgen},
-doi = {10.1023/A:1018320925954},
-journal = {Biodiversity and Conservation},
-number = {3},
-pages = {451--476},
-title = {{Alternative models of vertebrate speciation in Amazonia: An overview 8}},
-volume = {6},
-year = {1997}
-}
-@article{Palmer1994,
-abstract = {The complex relationship between species richness and area can be simplified by decomposing spatial scale into its components: grain, extent, and number of samples. We designed a 256 x 256-m study grid in the Oosting Natural Area in the Duke Forest, Orange County, North Carolina, such that the effects of these components can be disentangled. We found that grain, extent, and the number of samples all influenced the species-area relationship, although the effects of grain were dominant. We also found that species richness patterns were neither self-similar nor hierarchical. The degree to which diversity occurs in "hot spots" increases as a function of both grain and extent, but diversity hot spots tend to persist across a wide range of grains.},
-author = {Palmer, Michael W. and White, Peter S.},
-doi = {10.1086/285704},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Palmer, White - 1994 - Scale dependence and the species-area relationship.pdf:pdf},
-journal = {The American Naturalist},
-number = {5},
-pages = {717--740},
-title = {{Scale dependence and the species-area relationship}},
-url = {http://www.jstor.org/stable/2463009},
-volume = {144},
-year = {1994}
-}
-@article{Eckel2008,
-abstract = {The relative purchasing power-i.e., the purchasing power per inhabitant-is one of the key characteristics for businesses deciding on site selection. Apart from that it also plays a major role in regional planning, pricing policy and market research. In this study we investigate the spatial correlations for relative purchasing power of the townships in Baden-Wurttemberg. In particular, changes in relative purchasing power are analysed for three different time intervals, 1987-1993, 1993-1998 and 1998-2004, by means of distance-dependent characteristics like the mark-correlation function, the Simpson indices alpha(r) and beta(r) and by tests on random labelling. It is shown that there are positive correlations for small distances between different townships but that these positive correlations become weaker over the years until they are almost nonexistent (in the sense that hypotheses of random labelling are no longer rejected). A conclusion from this loss of spatial correlations with time is that the relative purchasing power might become more and more purely random. This means that the relative purchasing power in a township is less and less influenced by the relative purchasing power of townships nearby. We further analysed these changes in the Bodensee-Oberschwaben and Stuttgart regions to compare the development of the relative purchasing power in both urban and rural environments.},
-annote = {ISI Document Delivery No.: 302VM
-Times Cited: 1
-Cited Reference Count: 9
-Eckel, S. Fleischer, F. Grabarnik, P. Schmidt, V.
-Springer
-New york},
-author = {Eckel, S. and Fleischer, F. and Grabarnik, P. and Schmidt, V.},
-doi = {10.1007/s10182-008-0066-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eckel et al. - 2008 - An investigation of the spatial correlations for relative purchasing power in Baden-Wurttemberg.pdf:pdf},
-journal = {Asta-Advances in Statistical Analysis},
-number = {2},
-pages = {135--152},
-title = {{An investigation of the spatial correlations for relative purchasing power in Baden-Wurttemberg}},
-url = {https://link.springer.com/article/10.1007{\%}2Fs10182-008-0066-1},
-volume = {92},
-year = {2008}
-}
-@article{Arbia2016,
-abstract = {Spatial data are often contaminated with a series of imperfections that reduce their quality and can dramatically distort the inferential conclusions based on spatial econometric modeling. A “clean” ideal situation considered in standard spatial econometrics textbooks is when we fit Cliff-Ord-type models to data where the spatial units constitute the full population, there are no missing data, and there is no uncertainty on the spatial observations that are free from measurement and loca- tional errors. Unfortunately in practical cases the reality is often very different and the datasets contain all sorts of imperfections: They are often based on a sample drawn from the whole population, some data are missing and they almost invariably contain both attribute and locational errors. This is a situation of “dirty” spatial economet- ric modeling. Through a series of Monte Carlo experiments, this paper considers the effects on spatial econometric model estimation and hypothesis testing of two specific sources of dirt, namely missing data and locational errors.},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego},
-doi = {10.1007/s00168-015-0726-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia, Espa, Giuliani - 2016 - Dirty spatial econometrics.pdf:pdf},
-journal = {Annals of Regional Science},
-number = {1},
-pages = {177--189},
-title = {{Dirty spatial econometrics}},
-volume = {56},
-year = {2016}
-}
-@article{Dale2002,
-abstract = {A large number of methods for the analysis of the spatial structure of natural phenomena (for example, the clumping or overdispersion of tree stems, the positions of veins of ore in a rock formation, the arrangement of habitat patches in a landscape, and so on) have been developed in a wide range of scientific fields. This paper reviews many of the methods and describes the relationships among them, both mathematically, using the cross-product as a unifying principle, and conceptually, based on the form of a moving window or template used in calculation. The relationships among these methods suggest that while no single method can reveal all the important characteristics of spatial data, the results of different analyses are not expected to be completely independent of each other.},
-annote = {Cited By (since 1996): 142
-Export Date: 24 January 2012
-Source: Scopus
-CODEN: ECOGE
-Language of Original Document: English
-Correspondence Address: Dale, M.R.T.; Dept. of Biological Sciences, Univ. of Alberta, Edmonton, Alta. T6G 2E9, Canada; email: mark.dale@ualberta.ca},
-author = {Dale, Mark R.T. and Dixon, Philip M. and Fortin, Marie-Jos{\'{e}}e and Legendre, Pierre and Myers, Donald E. and Rosenberg, Michael S.},
-doi = {10.1034/j.1600-0587.2002.250506.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dale et al. - 2002 - Conceptual and mathematical relationships among methods for spatial analysis.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {558--577},
-title = {{Conceptual and mathematical relationships among methods for spatial analysis}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0036779314{\&}partnerID=40{\&}md5=e66dfe1f476a8bed3bc737a8ad9906fc},
-volume = {25},
-year = {2002}
-}
-@article{Barwell2015,
-abstract = {In 2003, 24 presence-absence $\beta$-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of $\beta$-diversity is lacking. $\beta$-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a $\beta$-diversity metric: metrics should be 1) independent of $\alpha$-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of $\beta$ than extreme 8) ranks shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry ($\beta$A,B=$\beta$B,A), 12) double-zero asymmetry for double-absences and double-presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer $\beta$-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five “personality” properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, $\beta$sim, performed well overall. Only $\beta$Baselga R turn, $\beta$Baselga B-C turn and $\beta$sim measured purely species turnover and were independent of nestedness. Among the other metrics, sensitivity to nestedness varied {\textgreater}4-fold. Our results indicate large amounts of redundancy among existing $\beta$-diversity metrics, while the estimation of unseen shared and unshared species is lacking and should be addressed in the design of new abundance-based metrics. This article is protected by copyright. All rights reserved.},
-author = {Barwell, Louise J. and Isaac, Nick J B and Kunin, William E.},
-doi = {10.1111/1365-2656.12362},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barwell, Isaac, Kunin - 2015 - Measuring beta-diversity with species abundance data.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {4},
-pages = {1112--1122},
-title = {{Measuring beta-diversity with species abundance data}},
-volume = {84},
-year = {2015}
-}
-@article{Tirado2003,
-abstract = {To link spatial patterns and ecological processes, we analysed the distribution of two shrub species (one large and dominant, the other smaller) and estimated the reproductive consequences of their distribution for the smaller species. We tested the significance of the spatial distribution pattern of the two shrubs by second-order bivariate point pattern analysis (Ripley's K function). Performance of Asparagus albus, the smaller shrub, was measured as (1) survival of transplanted seedlings in two contrasting habitats: patches of the dominant shrub (Ziziphus lotus), and open interspaces; and (2) reproductive output of plants naturally occurring in both habitats. The two species were significantly aggregated. Transplanted Asparagus albus seedlings had higher survival rates in patches than in the open. Plants produced more flowers, fruits, and showed a higher mass of seeds when living in aggregates than when isolated. The mechanisms responsible for this facilitative effect seem to be related to soil enrichment in patches. These results suggest that the spatial aggregation of species can be indicative of a positive interaction among them, directly affecting fitness of at least one of the species. Facilitation, by inducing variations in the reproductive performance may play a major role in the demography and dynamics of plant populations.},
-annote = {Article
-English
-OECOLOGIA
-700BJ},
-author = {Tirado, Reyes and Pugnaire, Francisco I.},
-doi = {10.1007/s00442-003-1264-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tirado, Pugnaire - 2003 - Shrub spatial aggregation and consequences for reproductive success.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {296--301},
-title = {{Shrub spatial aggregation and consequences for reproductive success}},
-url = {http://link.springer.com/article/10.1007/s00442-003-1264-x},
-volume = {136},
-year = {2003}
-}
-@article{Bickenbach2013,
-abstract = {Empirical studies on the evolution of concentration, specialization or localization of economic activity have provided ambiguous results that strongly depend on the researcher's choice of the reference. This paper develops a decomposition method for Theil indices of localization that clarifies where this ambiguity originates from. The method allows expressing the difference between absolute and relative Theil indices of localization in terms of Theil indices that are subject to straightforward interpretation. Illustrations show that the divergence of absolute from relative localization in the EU-15 and in UK manufacturing is largely a statistical artifact inherited from the peculiarities of the industry classifications.},
-annote = {Times Cited: 0
-Bickenbach, Frank Bode, Eckhardt Krieger-Boden, Christiane},
-author = {Bickenbach, Frank and Bode, Eckhardt and Krieger-Boden, C.},
-doi = {10.1111/j.1435-5957.2012.00460.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bickenbach, Bode, Krieger-Boden - 2013 - Closing the gap between absolute and relative measures of localization, concentration or specia.pdf:pdf},
-journal = {Papers in Regional Science},
-number = {3},
-pages = {465--480},
-title = {{Closing the gap between absolute and relative measures of localization, concentration or specialization}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1435-5957.2012.00460.x/abstract},
-volume = {92},
-year = {2013}
-}
-@article{Maurel1999,
-abstract = {The purpose of this paper is to offer an empirical investigation of the geographic concentration of French industries. The index of concentration is derived from a location model in the line of Ellison and Glaeser (1994, 1997) and can be interpreted as the correlation between the location decisions of two business units in the same industry. Along with extractive and traditional industries, some high technology industries are highly localized, which supports the view that technological spillovers may be important. Besides, the identification of the most and least localized industries reveals similar patterns in France and in the U.S.},
-author = {Maurel, Fran{\c{c}}oise and S{\'{e}}dillot, B{\'{e}}atrice},
-doi = {10.1016/S0166-0462(99)00020-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Maurel, S{\'{e}}dillot - 1999 - A Measure of the Geographic Concentration in French Manufacturing Industries.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {5},
-pages = {575--604},
-title = {{A Measure of the Geographic Concentration in French Manufacturing Industries}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046299000204},
-volume = {29},
-year = {1999}
-}
-@article{Ficetola2015,
-abstract = {Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.},
-author = {Ficetola, Gentile F. and Pansu, Johan and Bonin, Aur{\'{e}}lie and Coissac, Eric and Giguet-Covex, Charline and {De Barba}, Marta and Gielly, Ludovic and Lopes, Carla M. and Boyer, Fr{\'{e}}d{\'{e}}ric and Pompanon, Fran{\c{c}}ois and Ray{\'{e}}, Gilles and Taberlet, Pierre},
-doi = {10.1111/1755-0998.12338},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ficetola et al. - 2015 - Replication levels, false presences and the estimation of the presenceabsence from eDNA metabarcoding data.pdf:pdf},
-journal = {Molecular Ecology Resources},
-number = {3},
-pages = {543--556},
-title = {{Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data}},
-url = {http://doi.wiley.com/10.1111/1755-0998.12338},
-volume = {15},
-year = {2015}
-}
-@article{Schiffers2008,
-abstract = {Point pattern analyses such as the estimation of Ripley's K-function or the pair-correlation function g are commonly used in ecology to characterise ecological patterns in space. However, a major disadvantage of these methods is their missing ability to deal with spatial heterogeneity. A heterogeneous intensity of points causes a systematic bias in estimates of the K- and g-functions, a phenomenon termed "virtual aggregation" in the recent literature. To address this problem, we derive a new index, called K2-index, as an extension of existing point pattern characteristics. The K2-index has a heuristic interpretation as an approximation to the first derivative of the g-function. We estimate the K-, g- and K2-functions for six different types of simulated point patterns and show that the K2-index may provide important information on point patterns that the other methods fail to detect. The results indicate that particularly the small-scale distributions of points are better represented by the K2-index. This might be important for testing hypotheses on ecological processes, because most of these processes, such as direct neighbour interactions, occur very locally. When applied to empirical patterns of molehill distribution, the results of the K2-analysis show regularity up to distances between 0.1 and 0.4 m in most of the study areas, and aggregation of molehills up to distances between 0.2 and 1.1 m. The type and scale of these deviations from randomness agree with a priori expectations on the hill-building behaviour of moles. In contrast, the estimated g-functions merely indicate aggregation at the full range from 0 to 7 m (or even above). Considering the advantages and disadvantages of the different methods, we suggest that the K2-index should be used as a complement to existing approaches, particularly for point patterns generated by processes that act on more than one scale.},
-annote = {ISI Document Delivery No.: 356ZA
-Times Cited: 5
-Cited Reference Count: 56
-Schiffers, Katja Schurr, Frank M. Tielboerger, Katja Urbach, Carsten Moloney, Kirk Jeltsch, Florian
-WILEY-BLACKWELL},
-author = {Schiffers, Katja and Schurr, Frank M. and Tielborger, Katja and Urbach, Carsten and Moloney, Kirk A. and Jeltsch, Florian},
-doi = {10.1111/j.0906-7590.2008.05374.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schiffers et al. - 2008 - Dealing with virtual aggregation - a new index for analysing heterogeneous point patterns.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {545--555},
-title = {{Dealing with virtual aggregation - a new index for analysing heterogeneous point patterns}},
-volume = {31},
-year = {2008}
-}
-@article{Case1981,
-abstract = {A coevolutionary model of species packing is de-veloped that allows evolutionary adjustment in both niche position and within-phenotype niche width of one-three competing spe-cies. The environment is specified as a single resource dimension x and availability of resources along x is given by a gaussian curve that has parameters XR and oR. The model predicts that, for S species, the ratio of optimal niche width w to OR is roughly in-dependent of o7R and can be approximated by 1/S when the com-petitors are completely resource limited. Niche separation (d/W) increases only moderately with increases in resource di-versity c7R and is greater for two than for three competing species. To the extent that the competitors are not completely resource limited, both coevolutionary niche separation and niche width de-crease. Many of the general trends in niche width and niche sep-aration predicted by this coevolutionary model parallel those from optimal foraging theory and limiting similarity models of com-munity structure. The coevolutionary model stands out, however, in the singularly high values predicted for niche separation, mak-ing coevolved communities highly invasible. Hence, the theory suggests, as some empirical evidence indicates, that coevolved competition communities can only exist as such on remote islands or in other habitats that might be free from invasion by outside species. Niche theory (1) has enjoyed a tradition of success in ecology, largely because naturalists have been able to decipher the en-vironmental variables that are most limiting and critical to their chosen organisms ofstudy (1, 2). Often a single niche dimension (albeit sometimes a concocted one using multivariate statistical techniques) reveals a surprising amount of information about a particular ecological guild. Species niches assort, evenly and regularly along this dimension (e.g., altitude for birds or plants along a mountainside or prey size for raptors or lizards). Such regularity in niche dispersion is often taken as primafacie evi-dence that competition has been at work molding niches in the past, ifnot in the present (3). There have been two very different theoretical approaches to examining the way competition might lead to niche overdispersion. This question was first attacked theoretically by MacArthur and Levins (4) who used the "lim-iting similarity" paradigm to answer it. A single resource di-mension (x) is assumed, and the niches oftwo resident consumer species are described by utilization functionsf1(x) andf2(x) that},
-author = {Case, Ted J.},
-doi = {10.1073/pnas.78.8.5021},
-isbn = {0027-8424},
-issn = {0027-8424},
-journal = {Ecology},
-number = {8},
-pages = {5021--5025},
-pmid = {16593073},
-title = {{Niche packing and coevolution in competition communities}},
-volume = {78},
-year = {1981}
-}
-@article{Anderson2006,
-abstract = {Beta diversity can be defined as the variability in species composition among sampling units for a given area. We propose that it can be measured as the average dissimilarity from individual observation units to their group centroid in multivariate space, using an appropriate dissimilarity measure. Differences in beta diversity among different areas or groups of samples can be tested using this approach. The choice of transformation and dissimilarity measure has important consequences for interpreting results. For kelp holdfast assemblages from New Zealand, variation in species composition was greater in smaller holdfasts, while variation in relative abundances was greater in larger holdasts. Variation in community structure of Norwegian continental shelf macrobenthic fauna increased with increases in environmental heterogeneity, regardless of the measure used. We propose a new dissimilarity measure which allows the relative weight placed on changes in composition vs. abundance to be specified explicitly.},
-author = {Anderson, Marti J. and Ellingsen, Kari E. and McArdle, Brian H.},
-doi = {10.1111/j.1461-0248.2006.00926.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anderson, Ellingsen, McArdle - 2006 - Multivariate dispersion as a measure of beta diversity.pdf:pdf},
-journal = {Ecology letters},
-number = {6},
-pages = {683--93},
-title = {{Multivariate dispersion as a measure of beta diversity.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/16706913},
-volume = {9},
-year = {2006}
-}
-@article{Zhang2014,
-abstract = {This paper serves a twofold purpose. First, a unified perspective on diversity indices is introduced based on an entropic basis. It is shown that the class of all linear combinations of the entropic basis, referred to as the class of linear diversity indices, covers a wide range of diversity indices used in the literature. Second, a class of estimators for linear diversity indices is proposed and it is shown that these estimators have rapidly decaying biases and asymptotic normality.},
-author = {Zhang, Zhiyi and Grabchak, Michael},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Grabchak - 2016 - Entropic Representation and Estimation of Diversity Indices.pdf:pdf},
-journal = {Journal of Nonparametric Statistics},
-number = {3},
-pages = {563--575},
-title = {{Entropic Representation and Estimation of Diversity Indices}},
-volume = {28},
-year = {2016}
-}
-@article{Messier2010,
-abstract = {Despite the increasing importance of functional traits for the study of plant ecology, we do not know how variation in a given trait changes across ecological scales, which prevents us from assessing potential scale-dependent aspects of trait variation. To address this deficiency, we partitioned the variance in two key functional traits (leaf mass area and leaf dry matter content) across six nested ecological scales (site, plot, species, tree, strata and leaf) in lowland tropical rainforests. In both traits, the plot level shows virtually no variance despite high species turnover among plots and the size of within-species variation (leaf + strata + tree) is comparable with that of species level variation. The lack of variance at the plot level brings substantial support to the idea that trait-based environmental filtering plays a central role in plant community assembly. These results and the finding that the amount of within-species variation is comparable with interspecific variation support a shift of focus from species-based to trait-based ecology.},
-author = {Messier, Julie and McGill, Brian J. and Lechowicz, Martin J.},
-doi = {10.1111/j.1461-0248.2010.01476.x},
-file = {::},
-journal = {Ecology letters},
-number = {7},
-pages = {838--48},
-title = {{How do traits vary across ecological scales? A case for trait-based ecology}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/20482582},
-volume = {13},
-year = {2010}
-}
-@article{Mao2005,
-abstract = {We examine the role of rare species in the problem of estimating within-habitat species richness based on sampling data. Richness estimation can be modeled realistically for abundance-based and incidence-based data using Poisson or binomial mixtures, respectively. The problem can be reduced to estimation of the odds of the probability of a species remaining undetected in the sample or sample set.Within this rigorous statistical framework, we explore existing methods of richness estimation and assess their limitations. We do this by modeling the addition of increasing numbers of rare, undetected species to a reference assemblage, assessing the power of different methods to distinguish the modified species assemblages from the reference assemblage. (We use empirical example data sets for birds, seeds, and beetles as reference assemblages.) By considering the contributions of rare species and the role of undetected species for a fixed sampling effort, we show why the problem of richness estimation is so difficult, and we discuss what statistical models can provide.},
-author = {Mao, Chang Xuan and Colwell, Robert K.},
-doi = {10.1890/04-1078},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mao, Colwell - 2005 - Estimation of Species Richness Mixture Models, the Role of Rare Species, and Inferential Challenges.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1143--1153},
-title = {{Estimation of Species Richness: Mixture Models, the Role of Rare Species, and Inferential Challenges}},
-url = {http://dx.doi.org/10.1890/04-1078},
-volume = {86},
-year = {2005}
-}
-@article{Mouchet2011,
-abstract = {Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into $\alpha$, $\beta$ and $\gamma$ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating $\alpha$, $\beta$ and $\gamma$ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.},
-author = {Mouchet, Maud A. and Mouillot, David},
-doi = {10.1098/rsbl.2010.0769},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouchet, Mouillot - 2011 - Decomposing phylogenetic entropy into $\alpha$, $\beta$ and $\gamma$ components.pdf:pdf},
-journal = {Biology Letters},
-number = {2},
-pages = {205--209},
-title = {{Decomposing phylogenetic entropy into $\alpha$, $\beta$ and $\gamma$ components}},
-url = {http://rsbl.royalsocietypublishing.org/content/7/2/205.abstract},
-volume = {7},
-year = {2011}
-}
-@article{Colwell2012,
-abstract = {Aims: In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence-absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units. Methods: The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants. Important Findings: Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95{\%} confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature. {\textcopyright} 2012 The Author. Published by Oxford University Press on behalf of the Institute of Botany, Chinese Academy of Sciences and the Botanical Society of China. All rights reserved.},
-annote = {Export Date: 13 April 2012
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Colwell, R.K.; Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, United States; email: colwell@uconn.edu},
-author = {Colwell, Robert K. and Chao, Anne and Gotelli, Nicholas J. and Lin, Shang-Yi and Mao, Chang Xuan and Chazdon, Robin L. and Longino, John T.},
-doi = {10.1093/jpe/rtr044},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Colwell et al. - 2012 - Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of ass.pdf:pdf},
-journal = {Journal of Plant Ecology},
-number = {1},
-pages = {3--21},
-title = {{Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84855955478{\&}partnerID=40{\&}md5=8875226b44551fb89fac9985979e2fd3},
-volume = {5},
-year = {2012}
-}
-@article{Zhang2014a,
-abstract = {In this letter, we introduce an estimator of K{\"{u}}llback-Leibler divergence based on two independent samples. We show that on any finite alphabet, this estimator has an exponentially decaying bias and that it is consistent and asymptotically normal. To explain the importance of this estimator, we provide a thorough analysis of the more standard plug-in estimator. We show that it is consistent and asymptotically normal, but with an infinite bias. Moreover, if we modify the plug-in estimator to remove the rare events that cause the bias to become infinite, the bias still decays at a rate no faster than [Formula: see text]. Further, we extend our results to estimating the symmetrized K{\"{u}}llback-Leibler divergence. We conclude by providing simulation results, which show that the asymptotic properties of these estimators hold even for relatively small sample sizes.},
-author = {Zhang, Zhiyi and Grabchak, Michael},
-doi = {10.1162/NECO_a_00646},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Grabchak - 2014 - Nonparametric Estimation of Kullback-Leibler Divergence.pdf:pdf},
-journal = {Neural computation},
-number = {11},
-pages = {2570--2593},
-title = {{Nonparametric Estimation of Kullback-Leibler Divergence}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/25058703},
-volume = {26},
-year = {2014}
-}
-@article{Studeny2013,
-abstract = {1. The current headline indicator for ecosystem health and sustainability incorporates a geo- metric mean of relative abundances of breeding birds. Recently, a family of diversity mea- sures (k-measures) has been proposed as a novel instrument to separate diversity trends in dominant and rare species. This makes them an ecologically informative complement to cur- rent composite diversity indices. 2. Using both a geometric mean and the set of k-measures, we study habitat-specific tempo- ral trends in the diversity of British breeding birds. The analysis employs abundance estimates corrected for variation in detectability between individuals from different species to reduce bias. Applying generalized additive models, we predict long-term trends. We locate significant changes in these diversity trends. 3. While the geometric mean reveals overall diversity trends by habitat type, supplementing these by the k-measures provides a more nuanced picture of trends: a positive trend in the geometric mean may hide predominantly declining trends among the rarer species, which is then revealed by trends in the k-measures. 4. Synthesis and Applications. Bird populations are seen as useful indicators of the health of wildlife and the countryside because they occupy a range of habitats, they tend to be towards the top of the food chain, and data is provided by long-term surveys. Hence, many countries apply wild bird indicators (WBIs), quantifying trends in biodiversity, to monitor environmen- tal health. The UK's WBI, for example, has become one of the government's headline indica- tors of sustainable development. Understanding the population changes underlying the estimated trends is indispensable if we are to allocate limited resources more effectively. Employing a novel set of measures alongside the traditional geometric mean index, we ana- lyse diversity trends among British breeding birds. It reveals that species that are scarce, but not yet in the focus of conservation action, may be the ‘losers' in biodiversity action plans. This suggests that additional resources should be devoted to species showing long-term decline before they reach the low population levels that currently trigger large-scale species- specific rescue projects.},
-author = {Studeny, Angelika C. and Buckland, Stephen T. and Harrison, Philip J. and Illian, Janine B. and Magurran, Anne E. and Newson, Stuart E.},
-doi = {10.1111/1365-2664.12026},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Studeny et al. - 2013 - Fine-tuning the assessment of large-scale temporal trends in biodiversity using the example of British breeding.pdf:pdf},
-journal = {Journal of Applied Ecology},
-number = {1},
-pages = {190--198},
-title = {{Fine-tuning the assessment of large-scale temporal trends in biodiversity using the example of British breeding birds}},
-url = {http://doi.wiley.com/10.1111/1365-2664.12026},
-volume = {50},
-year = {2013}
-}
-@techreport{Zucker1994,
-abstract = {We examine the effects of university-based star scientists on three measures of performance for California biotechnology enterprises: the number of products in development, the number of products on the market, and changes in employment. The `star' concept which Zucker, Darby, and Brewer (1994) demonstrated was important for birth of U.S. biotechnology enterprises also predicts geographically localized knowledge spillovers at least for products in development. However, when we break down university stars into those who have collaborated on publications with scientists affiliated with the firm and all other university stars, there is a strong positive effect of the linked stars on all three firm-performance measures and little or no evidence of an effect from the other university stars. We develop a new hypothesis of geographically localized effects of university research which is consistent with market exchange: Geographically localized effects occur for scientific discoveries characterized by natural excludability, those which can be learned only by working with discoverers or others who have received the knowledge through working together in the laboratory. Natural excludability results in intellectual capital, a transitory form of human capital, embodied in particular scientists whose services must be employed in order to practice the discovery. Contractual and/or ownership relationships occur between firms and the university scientists with intellectual capital and importantly determine firm productivity and growth.},
-author = {Zucker, Lynne G. and Darby, Michael R. and Armstrong, Jeff},
-doi = {10.3386/w4946},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zucker, Darby, Armstrong - 1994 - Intellectual capital and the firm the technology of geographically localized knowledge spillovers.pdf:pdf},
-institution = {NBER Working Paper Series},
-title = {{Intellectual capital and the firm: the technology of geographically localized knowledge spillovers}},
-url = {http://www.nber.org/papers/w4946},
-year = {1994}
-}
-@article{Behrens2015,
-abstract = {We use detailed micro-geographic data to document the location patterns of Canadian manufacturing industries and changes in those patterns during the first decade of 2000. Depending on industry classifications and years, 40 to 60{\%} of industries are geographically localized, i.e., are spatially clustered relative to overall manufacturing. Although some industries are increasingly clustered, localization has generally decreased in Canada according to our measures. We further document the locational trends of small plants, young plants, and exporters. Their location patterns do not differ significantly from that of the other plants in their industries.},
-author = {Behrens, Kristian and Bougna, Th{\'{e}}ophile},
-doi = {10.1016/j.regsciurbeco.2015.01.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Behrens, Bougna - 2015 - An Anatomy of the Geographical Concentration of Canadian Manufacturing Industries.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-pages = {47--69},
-title = {{An Anatomy of the Geographical Concentration of Canadian Manufacturing Industries}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046215000034},
-volume = {51},
-year = {2015}
-}
-@article{Potts2004,
-abstract = {Dispersal-assembly theories of species coexistence posit that environmental factors play no role in explaining community diversity and structure. Dispersal-assembly theories shed light on some aspects of community structure such as species-area and species-abundance relationships. However, species' environmental associations also affect these measures of community structure. Measurements of species' niche breadth and overlap address this influence. Using a new continuous measure of niche and a dispersal-assembly null model that maintains species' niche breadth and aggregation, we tested two hypotheses assessing the effects of habitat heterogeneity on the ability of dispersal-assembly theories to explain community niche structure. We found that in both homogenous and heterogeneous environments dispersal-assembly theories cannot fully explain observed niche structure. The performance of the dispersal-assembly null models was particularly poor in heterogeneous environments. These results indicate that non-dispersal based mechanisms are in part responsible for observed community structure and measures of community structure which include species' environmental associations should be used to test theories of species diversity.},
-author = {Potts, Matthew D. and Davies, Stuart J. and Bossert, William H. and Tan, S. and Supardi, M. N. Nur},
-doi = {10.1007/s00442-004-1525-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Potts et al. - 2004 - Habitat heterogeneity and niche structure of trees in two tropical rain forests.pdf:pdf},
-journal = {Oecologia},
-number = {3},
-pages = {446--453},
-title = {{Habitat heterogeneity and niche structure of trees in two tropical rain forests}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs00442-004-1525-3},
-volume = {139},
-year = {2004}
-}
-@article{Doukhan2016,
-abstract = {We propose a general definition for weak dependence of point processes as an alternative to mixing definitions. We give examples of such weak dependent point processes for the families of Neyman Scott processes or Cox processes. For these processes, we consider the empirical estimator of the empty space function F(r). Using the general setting of the weak dependence property, we show the Central Limit Theorem for a vector of such statistics with different r. This completes results establishing the Central Limit Theorem under the Poisson process hypothesis.},
-author = {Doukhan, Paul and Lang, Gabriel},
-doi = {10.1080/02331888.2016.1153097},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Doukhan, Lang - 2016 - Weak dependence of point processes and application to second-order statistics.pdf:pdf},
-journal = {Statistics},
-number = {6},
-pages = {1221--1235},
-title = {{Weak dependence of point processes and application to second-order statistics}},
-url = {http://www.tandfonline.com/doi/full/10.1080/02331888.2016.1153097},
-volume = {50},
-year = {2016}
-}
-@article{Doria2008,
-abstract = {The origin and processes creating the high diversity of plant species in neotropical rain forests and their floristic composition and multistratitified forest structure are still uncertain. Here, we studied one of the most common leaf morphotypes of the Cerrej{\'{o}}n flora (middle-late Paleocene, ca. 60-58 Ma), Guajira, Colombia, that contains one of the oldest records of neotropical rain forest floras. Fifty-seven leaf specimens were carefully examined with a focus on general morphology, venation patterns, and cuticular characteristics. The analysis allowed us to recognize four new species that were assigned to the fossil-leaf genus Menispermites on the basis of an ovate leaf shape with cordate to truncate bases, actinodromous primary venation, brochidodromous secondary venation, percurrent tertiary venation, regular polygonal reticulate fourth and fifth venation, well-developed polygonal areoles, entire margin, and the presence of a fimbrial vein. This set of characters suggests a possible affinity with the pantropical angiosperm family Menispermaceae. The predominantly climbing habit of this family suggests that the Cerrej{\'{o}}n Paleocene tropical rain forest was already multistratified. These findings represent the earliest record for the family in northern South America.},
-author = {Doria, Gabriela and Jaramillo, Carlos a and Herrera, Fabiany},
-doi = {10.3732/ajb.2007216},
-journal = {American journal of botany},
-number = {8},
-pages = {954--73},
-title = {{Menispermaceae from the Cerrejon Formation, middle to late Paleocene, Colombia.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/21632418},
-volume = {95},
-year = {2008}
-}
-@article{Ripley1979,
-abstract = {Tests of “randomness” and methods of edge-correction for spatial point patterns are surveyed. The asymptotic distribution theory and power of tests based on the nearest-neighbour distances and estimates of the variance function are investigated.},
-author = {Ripley, Brian D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1979 - Tests of 'randomness' for spatial point patterns.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {3},
-pages = {368--374},
-title = {{Tests of 'randomness' for spatial point patterns}},
-url = {http://www.jstor.org/stable/2985065},
-volume = {41},
-year = {1979}
-}
-@book{Motyka1947,
-address = {Lublin, Poland},
-author = {Motyka, J.},
-publisher = {Nakladem universytftu Marii Curie-Sklodowskiej},
-title = {{O celach i metodach badan geobotanicznych. Sur les buts et les m{\'{e}}thodes des recherches g{\'{e}}obotaniques}},
-year = {1947}
-}
-@article{Tuomisto1995,
-abstract = {JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about},
-archivePrefix = {arXiv},
-arxivId = {10.1111/j.1461-0248.2009.01314.x},
-author = {Tuomisto, Hanna and Ruokolainen, Kalle and Kalliola, Risto and Linna, Ari and Danjoy, Walter and Rodriguez, Zoila},
-doi = {10.1126/science.269.5220.63},
-eprint = {j.1461-0248.2009.01314.x},
-isbn = {0036-8075},
-issn = {0036-8075},
-journal = {Source: Science, New Series},
-number = {5220},
-pages = {63--66},
-pmid = {17787706},
-primaryClass = {10.1111},
-title = {{Dissecting Amazonian Biodiversity}},
-url = {http://www.jstor.org/stable/2889152},
-volume = {269},
-year = {1995}
-}
-@article{Jombart2010,
-abstract = {Phylogenetic comparative methods have long considered phylogenetic signal as a source of statistical bias in the correlative analysis of biological traits. However, the main life-history strategies existing in a set of taxa are often combinations of life history traits that are inherently phylogenetically structured. In this paper, we present a method for identifying evolutionary strategies from large sets of biological traits, using phylogeny as a source of meaningful historical and ecological information. Our methodology extends a multivariate method developed for the analysis of spatial patterns, and relies on finding combinations of traits that are phylogenetically autocorrelated. Using extensive simulations, we show that our method efficiently uncovers phylogenetic structures with respect to various tree topologies, and remains powerful in cases where a large majority of traits are not phylogenetically structured. Our methodology is illustrated using empirical data, and implemented in the adephylo package for the free software R. {\textcopyright} 2010 Elsevier Ltd.},
-author = {Jombart, Thibaut and Pavoine, Sandrine and Devillard, S{\'{e}}bastien and Pontier, Dominique},
-doi = {10.1016/j.jtbi.2010.03.038},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jombart et al. - 2010 - Putting phylogeny into the analysis of biological traits A methodological approach.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {3},
-pages = {693--701},
-title = {{Putting phylogeny into the analysis of biological traits: A methodological approach}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519310001736},
-volume = {264},
-year = {2010}
-}
-@article{Walker1999,
-abstract = {This study tested an hypothesis concerning patterns in species abundance in ecological communities. Why do the majority of species occur in low abundance, with just a few making up the bulk of the biomass? We propose that many of the minor species are analogues of the dominants in terms of the ecosystem functions they perform, but differ in terms of their capabilities to respond to environmental stresses and disturbance. They thereby confer resilience on the community with respect to ecosystem function. Under changing conditions, ecosystem function is maintained when dominants decline or are lost because functionally equivalent minor species are able to substitute for them. We have tested this hypothesis with respect to ecosystem functions relating to global change. In particular, we identified five plant functional attributes—height, biomass, specific leaf area, longevity, and leaf litter quality—that determine carbon and water fluxes. We assigned values for these functional attributes to each of the graminoid species in a lightly grazed site and in a heavily grazed site in an Australian rangeland. Our resilience proposition was cast in the form of three specific hypotheses in relation to expected similarities and dissimilarities between dominant and minor species, within and between sites. Functional similarity—or ecological distance—was determined as the euclidean distance between species in functional attribute space. The analyses provide evidence in support of the resilience hypothesis. Specifically, within the lightly grazed community, dominant species were functionally more dissimilar to one another, and functionally similar species more widely separated in abundance rank, than would be expected on the basis of average ecological distances in the community. Between communities, depending on the test used, two of three, or three of four minor species in the lightly grazed community that were predicted to increase in the heavily grazed community did in fact do so. Although there has been emphasis on the importance of functional diversity in supporting the flow of ecosystem goods and services, the evidence from this study indicates that functional similarity (between dominant and minor species, and among minor species) may be equally important in ensuring persistence (resilience) of ecosystem function under changing environmental conditions.},
-author = {Walker, Brian and Kinzig, Ann and Langridge, Jenny},
-doi = {10.1007/s100219900062},
-journal = {Ecosystems},
-number = {2},
-pages = {95--113},
-title = {{Plant Attribute Diversity, Resilience, and Ecosystem Function: The Nature and Significance of Dominant and Minor Species}},
-url = {http://dx.doi.org/10.1007/s100219900062},
-volume = {2},
-year = {1999}
-}
-@book{Steppan1998,
-author = {Steppan, David D. and Werner, Joachim and Yeater, Robert P.},
-title = {{Essential Regression and Experimental Design for Chemists and Engineers}},
-url = {http://www.jowerner.homepage.t-online.de/ERPref.html},
-year = {1998}
-}
-@article{Pillar2013,
-abstract = {Questions: Functional redundancy in assemblages may insure ecosystem pro- cesses after perturbation, potentially causing temporary or permanent local spe- cies extinctions. Yet, functional redundancy has only been inferred by indirect evidence or measured by methods that may not be the most appropriate. Here, we apply an existing method to measure functional redundancy, which is the fraction of species diversity not expressed by functional diversity, to assess whether functional redundancy affects community resilience after disturbance. Location: Subtropical grassland, south Brazil (30°05′46″S, 51°40′37″W). Method: Species traits and community composition were assessed in quadrats before grazing and after community recovery. Grazing intensity (G)was mea- sured in each quadrat.We used traits linked to grazing intensity to define func- tional redundancy (FR)asthe difference of Gini–Simpson index of species diversity (D) and Rao's quadratic entropy (Q). Also, with the same traits, we defined community functional stability (S) as the similarity between trait-based community composition before grazing and 47 and 180 d after grazing ending. Using path analysis we assessed different postulated causal models linking functional diversity (Q), functional redundancy (FR), grazing intensity (G)and community-weightedmean traits to community stability (S) under grazing. Results: Path analysis revealed themost valid causal model FR ? S G,with a significant positive path coefficient for FR ? S and a marginally significant negative one for S G.Since FR and G were independent in their covariation and in their effects on S, themodel discriminated community resistance to graz- ing (the effect of G on S) from community resilience after grazing caused by functional redundancy (indicated by the effect of FR on S). Conclusion:We showthat expressing functional redundancymathematically is a useful tool for testing causal models linking diversity to community stability. The results support the conclusion that functional redundancy enhanced com- munity resilience, therefore corroborating the insurance hypothesis.},
-author = {Pillar, Val{\'{e}}rio D. and Blanco, Carolina C. and M{\"{u}}ller, Sandra C. and Sosinski, Enio E. and Joner, Fernando and Duarte, Leandro D. S.},
-doi = {10.1111/jvs.12047},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pillar et al. - 2013 - Functional redundancy and stability in plant communities.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {963--974},
-title = {{Functional redundancy and stability in plant communities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/jvs.12047/full},
-volume = {24},
-year = {2013}
-}
-@article{Galiano1982,
-abstract = {A method of sampling and analysis is proposed to detect pattern parameters in plant populations from two-dimensional data. The use of aerial photographs to find the coordinates of trees and the measurements of plant-to-all-plants distances yields conditioned probability spectra which can be interpreted in terms of pattern parameters. Two artificial populations and a set of real data have been analysed to test the accuracy of the method.},
-author = {Galiano, E. F.},
-doi = {10.1007/BF00051564},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Galiano - 1982 - Pattern Detection in Plant Populations through the Analysis of Plant-to-All-Plants Distances.pdf:pdf},
-journal = {Vegetatio},
-number = {1},
-pages = {39--43},
-title = {{Pattern Detection in Plant Populations through the Analysis of Plant-to-All-Plants Distances}},
-url = {http://link.springer.com/article/10.1007/BF00051564},
-volume = {49},
-year = {1982}
-}
-@article{Eviner2003,
-abstract = {Plant species differ in how they influence many aspects of ecosystem structure and function, including soil characteristics, geomorphology, biogeochemistry, regional climate, and the activity and distribution of other organisms. Attempts to generalize plant species effects on ecosystems have focused on single traits or suites of traits that strongly covary (functional groups). However, plant effects on any ecosystem process are mediated by multiple traits, and many of these traits vary independently from one another. Thus, most species have unique combinations of traits that influence ecosystems, and there is no single trait or functional-group classification that can capture the effects of these multiple traits, or can predict the multiple functions performed by different plant species. We present a new theoretical framework, the functional matrix, which builds upon the functional group and single trait approaches to account for the ecosystem effects of multiple traits that vary independently among species. The functional matrix describes the relationship between ecosystem processes and multiple traits, treating traits as continuous variables, and determining if the effects of these multiple traits are additive or interactive. The power of this approach is that the ecosystem effects of multiple traits are the underlying mechanisms determining species effects, how the effects of an individual species change across seasons and under varying environmental conditions, the nonadditive effects of plant species mixtures, and the effects of species diversity.},
-author = {Eviner, Valerie T. and Chapin, F. Stuart III},
-doi = {10.1146/annurev.ecolsys.34.011802.132342},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eviner, Chapin - 2003 - Functional Matrix A Conceptual Framework for Predicting Multiple Plant Effects on Ecosystem Processes.pdf:pdf},
-journal = {Annual Review of Ecology, Evolution, and Systematics},
-pages = {455--485},
-title = {{Functional Matrix: A Conceptual Framework for Predicting Multiple Plant Effects on Ecosystem Processes}},
-volume = {34},
-year = {2003}
-}
-@article{Ashbridge2000,
-abstract = {Consideration of coverage yields a new class of estimators of population size for the standard mark-recapture model which permits heterogeneity of capture probabilities. Real data and simulation studies are used to assess these coverage-adjusted estimators. The simulations highlight the need for estimators that perform well for a wide range of values of the mean and coefficient of variation of the capture probabilities. When judged for this type of robustness, the simulations provide good grounds for preferring the new estimators to earlier ones for this model, except when the number of sampling occasions is large. A bootstrapping approach is used to estimate the standard errors of the new estimators, and to obtain confidence intervals for the population size.},
-author = {Ashbridge, J. and Goudie, Ian B. J.},
-doi = {10.1080/03610910008813661},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ashbridge, Goudie - 2000 - Coverage-adjusted estimators for mark-recapture in heterogeneous populations.pdf:pdf},
-journal = {Communications in Statistics - Simulation and Computation},
-number = {4},
-pages = {1215--1237},
-title = {{Coverage-adjusted estimators for mark-recapture in heterogeneous populations}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/03610910008813661},
-volume = {29},
-year = {2000}
-}
-@incollection{Tilman2001a,
-address = {San Diego},
-author = {Tilman, David},
-booktitle = {Encyclopedia of Biodiversity},
-editor = {Levin, Simon},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tilman - 2001 - Functional diversity.pdf:pdf},
-pages = {109--121},
-publisher = {Academic Press},
-title = {{Functional diversity}},
-year = {2001}
-}
-@article{Hanson2001,
-abstract = {In recent empirical literature on spatial agglomeration, many papers find evidence consistent with location‐specific externalities of some sort. Our willingness to accept evidence of agglomeration economies depends on how well key estimation problems have been addressed. Three issues are particularly troublesome for identifying agglomeration effects: unobserved regional characteristics, simultaneity in regional data, and multiple sources of externalities. Two empirical results appear to be robust to problems created by the first two issues: (a) individual wages are increasing in the presence of more‐educated workers in the local labor force, which is consistent with localized human‐capital externalities, and (b) long‐run industry growth is higher in locations with a wider range of industrial activities, which suggests that firms benefit from being in more diverse urban environments. Other evidence is supportive of agglomeration effects related to regional demand linkages and short‐run, industry‐specific externalities.},
-author = {Hanson, Gordon H.},
-doi = {10.1093/jeg/1.3.255},
-journal = {Journal of Economic Geography},
-number = {3},
-pages = {255--276},
-title = {{Scale economies and the geographic concentration of industry}},
-url = {https://doi.org/10.1093/jeg/1.3.255},
-volume = {1},
-year = {2001}
-}
-@article{Keylock2005,
-abstract = {Many indices for measuring species diversity have been proposed. In this article, a link is noted between a common family of diversity indices and non-additive statistical mechanics. This makes the Shannon index and the Simpson diversity (or Gini coefficient) special cases of a more general index. The general index includes a parameter q that can be interpreted from a statistical mechanics perspective for systems with an underlying (multi) fractal structure. A q-generalised version of the Zipf-Mandelbrot distribution sometimes used to characterise rank-abundance relationships may be obtained by maximising this entropy.},
-annote = {Times Cited: 10},
-author = {Keylock, C. J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Keylock - 2005 - Simpson diversity and the Shannon-Wiener index as special cases of a generalized entropy.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {203--207},
-title = {{Simpson diversity and the Shannon-Wiener index as special cases of a generalized entropy}},
-volume = {109},
-year = {2005}
-}
-@article{Mori2013,
-abstract = {Dating from the seminal work of Ellison and Glaeser in 1997, a wealth of evidence for the ubiquity of industrial agglomerations has been published. However, most of these results are based on analyses of single (scalar) indices of agglomeration. Hence, it is not surprising that industries deemed to be similar by such indices can often exhibit very different patterns of agglomeration—with respect to the number, size and spatial extent of individual agglomerations. The purpose of this article is thus to propose a more detailed spatial analysis of agglomeration in terms of multiple-cluster patterns, where each cluster represents a (roughly) convex set of contiguous regions within which the density of establishments is relatively uniform. The key idea is to develop a simple probability model of multiple clusters, called cluster schemes, and then to seek a ‘best' cluster scheme for each industry by employing a standard model-selection criterion. Our ultimate objective is to provide a richer characterization of spatial agglomeration patterns that will allow more meaningful comparisons of these patterns across industries. Keywords:},
-author = {Mori, Tomoya and Smith, Tony E.},
-doi = {10.1093/jeg/lbs062},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mori, Smith - 2013 - A probabilistic modeling approach to the detection of industrial agglomerations.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {3},
-pages = {547--588},
-title = {{A probabilistic modeling approach to the detection of industrial agglomerations}},
-url = {http://joeg.oxfordjournals.org/cgi/doi/10.1093/jeg/lbs062},
-volume = {14},
-year = {2014}
-}
-@article{Alfaro2014,
-author = {Alfaro, Laura and Chen, Maggie Xiaoyang},
-doi = {10.1016/j.jinteco.2014.09.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alfaro, Chen - 2014 - The global agglomeration of multinational firms.pdf:pdf},
-issn = {00221996},
-journal = {Journal of International Economics},
-month = {oct},
-pages = {263--276},
-title = {{The global agglomeration of multinational firms}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0022199614001123},
-volume = {94},
-year = {2014}
-}
-@article{Pielou1966,
-abstract = {A measurable property of any collection of organisms containing more than one species is its “species-diversity”. Methods of measuring species-diversity based on the information content of a collection are reviewed. A collection consisting of a community of sessile organisms, such as terrestrial plants, also has “pattern-diversity”. The pattern-diversity of a community is high when the individuals of the various species are thoroughly mingled so that several species are usually present in any small sub-area; it is low if the species are segregated so that small sub-areas are likely to contain individuals of only a few of the species. A method of measuring pattern-diversity is proposed. The changes that occurred in both species- and pattern-diversity, during periods of five or ten years, in young dense communities of forest trees were observed. It was found that the natural thinning resulting from competition among the trees caused an increase in pattern-diversity.},
-author = {Pielou, Evelyn C.},
-doi = {10.1016/0022-5193(66)90133-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1966 - Species-diversity and pattern-diversity in the study of ecological succession.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {2},
-pages = {370--383},
-title = {{Species-diversity and pattern-diversity in the study of ecological succession}},
-url = {http://www.sciencedirect.com/science/article/pii/0022519366901330},
-volume = {10},
-year = {1966}
-}
-@misc{Rosenzweig1995,
-abstract = {Page 1. Species diversity in space and time Michael L Rosenzweig Page 2. Page 3. Why do larger areas have more species? What makes},
-author = {Rosenzweig, M},
-booktitle = {Cambridge University Press},
-title = {{Species diversity in space and time}},
-url = {http://books.google.com/books?hl=en{\&}lr={\&}id=RbOYBr0M{\_}wgC{\&}oi=fnd{\&}pg=PP15{\&}dq=beta-diversity+review{\&}ots=yk4up5t9Db{\&}sig=M5to2BXjUtCaf0fcS5IedVHRqHI},
-year = {1995}
-}
-@article{Guan2010,
-abstract = {We introduce a new estimation method for parametric intensity function models of inhomogeneous spatial point processes based on weighted estimating equations. The weights can incorporate information on both inhomogeneity and dependence of the process. Simulations show that significant efficiency gains can be achieved for non-Poisson processes, compared to the Poisson maximum likelihood estimator. An application to tropical forest data illustrates the use of the proposed method. {\textcopyright} 2010 Biometrika Trust.},
-annote = {cited By (since 1996) 1},
-author = {Guan, Yongtao and Shen, Ye},
-doi = {10.1093/biomet/asq043},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan, Shen - 2010 - A weighted estimating equation approach for inhomogeneous spatial point processes.pdf:pdf},
-journal = {Biometrika},
-number = {4},
-pages = {867--880},
-title = {{A weighted estimating equation approach for inhomogeneous spatial point processes}},
-volume = {97},
-year = {2010}
-}
-@article{Paine1969,
-author = {Paine, R. T.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Paine - 1969 - A note on trophic complexity and community stability.pdf:pdf},
-journal = {American naturalist},
-number = {929},
-pages = {91--93},
-title = {{A note on trophic complexity and community stability}},
-url = {http://www.jstor.org/stable/2459472},
-volume = {103},
-year = {1969}
-}
-@article{Arbia2012,
-abstract = {Why do industrial clusters occur in space? Is it because industries need to stay close together to interact or, conversely, because they concentrate in certain portions of space to exploit favourable conditions like public incentives, proximity to communication networks, to big population concentrations or to reduce transport costs? This is a fundamental question and the attempt to answer to it using empirical data is a challenging statistical task. In economic geography scientists refer to this dichotomy using the two categories of spatial interaction and spatial reaction to common factors. In economics we can refer to a distinction between exogenous causes and endogenous effects. In spatial econometrics and statistics we use the terms of spatial dependence and spatial heterogeneity. A series of recent papers introduced explorative methods to analyse the spatial patterns of firms using micro data and characterizing each firm by its spatial coordinates. In such a setting a spatial distribution of firms is seen as a point pattern and an industrial cluster as the phenomenon of extra-concentration of one industry with respect to the concentration of a benchmarking spatial distribution. Often the benchmarking distribution is that of the whole economy on the ground that exogenous factors affect in the same way all branches. Using such an approach a positive (or negative) spatial dependence between firms is detected when the pattern of a specific sector is more aggregated (or more dispersed) than the one of the whole economy. In this paper we suggest a parametric approach to the analysis of spatial heterogeneity, based on the so-called inhomogeneous K-function (Baddeley et al., 2000). We present an empirical application of the method to the spatial distribution of high-tech industries in Milan (Italy) in 2001. We consider the economic space to be non homogenous, we estimate the pattern of inhomogeneity and we use it to separate spatial heterogeneity from spatial dependence.},
-annote = {doi: 10.1016/j.econmod.2011.01.012},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego and Mazzitelli, A.},
-doi = {10.1016/j.econmod.2011.01.012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2012 - Clusters of firms in an inhomogeneous space The high-tech industries in Milan.pdf:pdf},
-journal = {Economic Modelling},
-number = {1},
-pages = {3--11},
-title = {{Clusters of firms in an inhomogeneous space: The high-tech industries in Milan}},
-url = {http://www.sciencedirect.com/science/article/pii/S0264999311000150},
-volume = {29},
-year = {2012}
-}
-@article{Williamson2005,
-abstract = {1 Of the many models for species–abundance distributions (SADs), the lognormal has been the most popular and has been put forward as an appropriate null model for testing against theoretical SADs. In this paper we explore a number of reasons why the lognormal is not an appropriate null model, or indeed an appropriate model of any sort, for a SAD. 2 We use three empirical examples, based on published data sets, to illustrate features of SADs in general and of the lognormal in particular: the abundance of British breeding birds, the number of trees {\textgreater} 1 cm diameter at breast height (d.b.h.) on a 50 ha Panamanian plot, and the abundance of certain butterflies trapped at Jatun Sacha, Ecuador. The first two are complete enumerations and show left skew under logarithmic transformation, the third is an incomplete enumeration and shows right skew. 3 Fitting SADs by ?2 test is less efficient and less informative than fitting probability plots. The left skewness of complete enumerations seems to arise from a lack of extremely abundant species rather than from a surplus of rare ones. One consequence is that the logit-normal, which stretches the right-hand end of the distribution, consistently gives a slightly better fit. 4 The central limit theorem predicts lognormality of abundances within species but not between them, and so is not a basis for the lognormal SAD. Niche breakage and population dynamical models can predict a lognormal SAD but equally can predict many other SADs. 5 The lognormal sits uncomfortably between distributions with infinite variance and the log-binomial. The latter removes the absurdity of the invisible highly abundant half of the individuals abundance curve predicted by the lognormal SAD. The veil line is a misunderstanding of the sampling properties of the SAD and fitting the Poisson lognormal is not satisfactory. A satisfactory SAD should have a thinner right-hand tail than the lognormal, as is observed empirically. 6 The SAD for logarithmic abundance cannot be Gaussian.},
-author = {Williamson, Mark and Gaston, Kevin J.},
-doi = {10.1111/j.1365-2656.2005.00936.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Williamson, Gaston - 2005 - The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {2001},
-pages = {409--422},
-title = {{The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2005.00936.x/abstract},
-volume = {74},
-year = {2005}
-}
-@article{Ricotta2010,
-abstract = {There are many different metrics for expressing the dissimilarity between two samples or plots. The large majority of these dissimilarity measures attempt to summarize different aspects of plot-to-plot dissimilarity based either on species presences and absences within plots or on species abundances. Here, we propose a new parametric measure of plot-to-plot functional dissimilarity that incorporates information about the degree of functional dissimilarity between species. This measure is obtained from the combination of Hurlbert's 'expected species diversity' with one dissimilarity coefficient of the 'Bray-Curtis family' and calculates the expected functional dissimilarity between the species in plot A and their functional nearest neighbors in plot B if m individuals are chosen randomly with replacement from each of the two plots. Due to its parametric nature, the proposed measure has a different sensitivity to the presence of rare and abundant species within plots as a function of the selected parameter value.},
-annote = {Pb de param{\'{e}}trage dans l'eq. 15. La contribution de l'esp{\`{e}}ce i {\`{a}} l'indice de Hurlbert (pi{\_}i(m)) ne correspond pas ce qu'on cherche: augmenter m n'augmente pas le poids des esp{\`{e}}ces rares.},
-author = {Ricotta, Carlo and Bacaro, Giovanni},
-doi = {10.1556/ComEc.11.2010.1.16},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Bacaro - 2010 - On plot-to-plot dissimilarity measures based on species functional traits.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {113--119},
-title = {{On plot-to-plot dissimilarity measures based on species functional traits}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77953823587{\&}partnerID=40{\&}md5=19955f00eb0c181fd6476014344489ea},
-volume = {11},
-year = {2010}
-}
-@article{Reeve2014,
-abstract = {The aim of partitioning biodiversity within an ecosystem is to identify dissimilarities in the species compositions of its constituent communities, but current approaches lack the critically important ability to account for similarities among species. Any new approach to diversity analysis must not only satisfy theoretical concerns, but also enable us to carry out real-world tasks such as fairly comparing different aspects of the biodiversity of communities, understanding how the community structure changes over time, and helping to identify the mechanisms that drive these processes. We propose new measures of alpha and beta diversity, sensitive to species similarity, that emerge naturally from recent similarity-sensitive gamma diversity measures. Our key advance is the decomposition of all three of these diversity measures into components reflecting the uniqueness of each community within the ecosystem, and their relative contributions to total ecosystem diversity. These provide powerful tools to reveal biologically important communities within an ecosystem, to assess the spatial and temporal variation in diversity, and to thereby identify the ecosystem's true underlying community structure and dynamics.},
-archivePrefix = {arXiv},
-arxivId = {1404.6520},
-author = {Reeve, R. and Matthews, L. and Cobbold, Christina and Leinster, Tom and Thompson, Jill and Brummitt, Neil},
-eprint = {1404.6520},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reeve et al. - 2014 - How to partition diversity.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{How to partition diversity}},
-url = {http://arxiv.org/abs/1404.6520},
-volume = {1404.6520},
-year = {2014}
-}
-@article{Edman2001,
-abstract = {Since many wood-living forest species are influenced by the dynamics of coarse woody debris (CWD), information about the spatial pattern of CWD under natural conditions is essential to understand species distributions. In this study we examined the spatial pattern of downed logs and wood-decaying fungi in an old-growth boreal Picea abies forest in northwestern Sweden that is governed by gap-phase dynamics. The spatial pattern of wood-decaying fungi was studied to draw conclusions about species dispersal abilities. A total of 684 logs with a diameter {\textgreater} 10 cm were mapped and analysed with Ripley's K-function. The distribution of all logs taken together displayed a significant aggregated pattern up to 45 m. The different decay stages also deviated from random expectations. Fairly fresh logs and logs in the middle decay stage were clumped up to about 25 and 35 m respectively, and late decayed logs aggregated up to 95 m. Logs with diameters from 10–29 cm were aggregated up to 25 m, whereas logs ≥30 cm diameter were randomly distributed. The result suggests that gap-dynamics do have an impact on the spatial pattern of the CWD, creating fine-scale clumping. The random distribution of large logs may result from the slightly regular spacing of large living trees. The spatial patterns of 16 species (n {\textgreater} 20) of wood-decaying fungi were analysed with Ripley's K-function. Three patterns were aggregated, for Gloeophyllum sepiarium, Coniophora olivacea and Vesiculomyces citrinus. These results indicate that the distribution of most species at the stand level is generally not influenced by dispersal limitations.},
-author = {Edman, M and Jonsson, B G},
-doi = {10.2307/3236900},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Edman, Jonsson - 2001 - Spatial pattern of downed logs and wood-decaying fungi in an old-growth Picea abies forest.pdf:pdf},
-journal = {Journal of Vegetation Science},
-keywords = {Edman (2001).pdf},
-mendeley-tags = {Edman (2001).pdf},
-number = {5},
-pages = {609--620},
-title = {{Spatial pattern of downed logs and wood-decaying fungi in an old-growth Picea abies forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236900/abstract},
-volume = {12},
-year = {2001}
-}
-@article{Peres-Neto2017,
-abstract = {Establishing trait-environment relationships has become routine in community ecology. Here, we demonstrate that the Community Weighted Means correlation (CWM) and its parallel approach in linking trait variation to the environment, the Species Niche Centroid correlation (SNC), have important shortcomings, arguing against their continuing application. Using mathematical derivations and simulations, we show that the two major issues are inconsistent parameter estimation and unacceptable significance rates when only the environment or only traits are structuring species distributions, but they themselves are not linked. We show how both CWM and SNC are related to the fourth-corner correlation and propose to replace all by the Chessel fourth-corner correlation, which is the fourth-corner correlation divided by its maximum attainable value. We propose an appropriate hypothesis testing procedure that is not only unbiased but also has much greater statistical power in detecting trait-environmental relationships. We derive an additive framework in which trait variation is partitioned among and within communities, which can be then modeled against the environment. We finish by presenting a contrast between methods and an application of our proposed framework across 85 lake-fish metacommunities.This article is protected by copyright. All rights reserved.},
-author = {Peres-Neto, Pedro R. and Dray, St{\'{e}}phane and ter Braak, Cajo J. F.},
-doi = {10.1111/ecog.02302},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peres-Neto, Dray, ter Braak - 2017 - Linking trait variation to the environment critical issues with community-weighted mean correlation.pdf:pdf},
-journal = {Ecography},
-number = {7},
-pages = {806--816},
-title = {{Linking trait variation to the environment: critical issues with community-weighted mean correlation resolved by the fourth-corner approach}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02302/abstract},
-volume = {40},
-year = {2017}
-}
-@article{Coyne2012,
-abstract = {American resistance to accepting evolution is uniquely high among First World countries. This is due largely to the extreme religiosity of the United States, which is much higher than that of comparably advanced nations, and to the resistance of many religious people to the facts and supposed implications of evolution. The prevalence of religious belief in the United States suggests that outreach by scientists alone will not have a huge effect in increasing the acceptance of evolution, nor will the strategy of trying to convince the faithful that evolution is compatible with their religion. Because creationism is a symptom of religion, another strategy to promote evolution involves loosening the grip of faith on America. This is easier said than done, for recent sociological surveys show that religion is highly correlated with the dysfunctionality of a society, and various measures of societal health show that the United States is one of the most socially dysfunctional First World countries. Widespread acceptance of evolution in America, then, may have to await profound social change.},
-author = {Coyne, Jerry A.},
-doi = {10.1111/j.1558-5646.2012.01664.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coyne - 2012 - Science, religion, and society the problem of evolution in America.pdf:pdf},
-journal = {Evolution},
-number = {8},
-pages = {2654--63},
-title = {{Science, religion, and society: the problem of evolution in America.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/22834762},
-volume = {66},
-year = {2012}
-}
-@article{Sichel1975,
-abstract = {In the past, several attempts were made to represent word frequency counts by statistical distribution laws. Of the models suggested, none was singularly successful when applied to a variety of data over the entire length of the observed word distributions. In this article, a new family of compound Poisson distributions 9, 10 is proposed as a model for word frequency counts. Twenty observed distributions quoted in the literature were fitted and the results look most encouraging.},
-author = {Sichel, H. S.},
-doi = {10.2307/2285930},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sichel - 1975 - On a Distribution Law for Word Frequencies.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {351},
-pages = {542--547},
-title = {{On a Distribution Law for Word Frequencies}},
-url = {http://www.jstor.org/stable/2285930?origin=crossref},
-volume = {70},
-year = {1975}
-}
-@article{Bernstein1988,
-author = {Bernstein, Jeffrey I. and Nadiri, M. Ishaq},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bernstein, Nadiri - 1988 - Interindustry R{\&}D Spillovers, Rates of Return, and Production in High-Tech Industries.pdf:pdf},
-journal = {The American Economic Review},
-number = {2},
-pages = {429--434},
-title = {{Interindustry R{\&}D Spillovers, Rates of Return, and Production in High-Tech Industries}},
-url = {https://www.jstor.org/stable/1818163},
-volume = {78},
-year = {1988}
-}
-@article{Kelly2004,
-abstract = {The impact of human activities on size class distribution and spatial distribution of Vitellaria paradoxa (karite or shea butter tree) in the parklands of sub-Saharan Africa has not been reported in the literature. Two sites (Koumantou and Mperesso) in southern Mali and three treatments ( cultivated field, fallow and forest) per site were involved in the present study. Results of a statistical test for random distribution showed that the spatial pattern of Vitellaria paradoxa became progressively aggregated from cultivated field to fallow and then to forest. A permanent aggregated pattern found at Koumantou was not found at Mperesso. A test of the independence of larger and smaller tree locations shows that size classes clump together at Koumantou but not at Mperesso. Results of the third test showed that in the cultivated field, auto-correlation was only observed at large scale. In the fallow the trend was towards negative correlation for both sites. In the forest, negative correlation was observed up to 20 m at Koumantou whereas at Mperesso, positive correlation was observed around 35 m and above 50 m. Site differences may be explained by the intensity of fruit production and recruitment, bound to rainfall and land use pressure. Greater regularity of the spatial pattern in cultivated field, then fallow, may be the result of human intervention.},
-annote = {Article},
-author = {Kelly, B. A. and Bouvet, Jean-Marc and Picard, Nicolas},
-doi = {10.1023/B:AGFO.0000009400.24606.e3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kelly, Bouvet, Picard - 2004 - Size class distribution and spatial pattern of Vitellaria paradoxa in relation to farmers' practices in M.pdf:pdf},
-journal = {Agroforestry Systems},
-number = {1},
-pages = {3--11},
-title = {{Size class distribution and spatial pattern of Vitellaria paradoxa in relation to farmers' practices in Mali}},
-url = {http://link.springer.com/article/10.1023/B:AGFO.0000009400.24606.e3},
-volume = {60},
-year = {2004}
-}
-@article{Tuomisto2014a,
-abstract = {The number of species is known to decrease from the humid tropics towards drier and colder climates, but how species richness varies along environmental and spatial gradients within the tropical rain forests is not clear. We inventoried 214 transects of 0.25 ha to document species diversity patterns in an example plant group (ferns and lycophytes) across non-inundated rain forests of western and central Amazonia, and assessed how well these conformed with proposed hypotheses about species richness. The observed number of species varied between 6 and 71 per transect. The effective number of species (emphasising the degree of unevenness in species abundances) varied between 1.02 and 8.60, and diversity profiles revealed considerable differences among transects in community structure. Although the density of individuals varied over almost two orders of magnitude, species diversity was better explained by other variables. In particular, within-transect species diversity increased substantially with increasing soil cation concentration. It also increased with soil aluminium concentration, heterogeneity in soil chemistry, annual rainfall and dry season rainfall, and was higher in western than in central Amazonia. Multiple regression models explained up to 70{\%} of the variance in species diversity, but the relationships between species diversity and the environmental gradients became progressively weaker as species abundances were given more weight in the calculation of diversity. Our results conformed to the proposal that site productivity promotes species diversity. This seemed to arise from larger species pools on more fertile soils and in wetter climates, even when it could be expected that the older and more widespread infertile soils would have provided more opportunities for speciation.},
-author = {Tuomisto, Hanna and Zuquim, Gabriela and C{\'{a}}rdenas, Glenda},
-doi = {10.1111/ecog.00770},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto, Zuquim, C{\'{a}}rdenas - 2014 - Species richness and diversity along edaphic and climatic gradients in Amazonia(2).pdf:pdf},
-journal = {Ecography},
-number = {11},
-pages = {1034--1046},
-title = {{Species richness and diversity along edaphic and climatic gradients in Amazonia}},
-url = {http://doi.wiley.com/10.1111/ecog.00770},
-volume = {37},
-year = {2014}
-}
-@article{Tsallis1998a,
-abstract = {Through the use of a recently introduced, nonextensive, entropy, we generalize that of Kullback and Leibler [Ann. Math. Stat. 22, 79 (1961)] and study its properties. This in turn enables the proposal of a consistent criterion for testing relevant hypotheses such as the independence of random variables. Straightforward applications are shown to be possible for (physical, geophysical, economic, and biological) time series.},
-annote = {PRE},
-author = {Tsallis, Constantino},
-doi = {10.1103/PhysRevE.58.1442},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsallis - 1998 - Generalized entropy-based criterion for consistent testing.pdf:pdf},
-journal = {Physical Review E},
-number = {2},
-pages = {1442--1445},
-title = {{Generalized entropy-based criterion for consistent testing}},
-url = {http://link.aps.org/doi/10.1103/PhysRevE.58.1442},
-volume = {58},
-year = {1998}
-}
-@article{Ahmed2013,
-abstract = {Past global climate changes had strong regional expression. To elucidate their spatio-temporal pattern, we reconstructed past temperatures for seven continental-scale regions during the past one to two millennia. The most coherent feature in nearly all of the regional temperature reconstructions is a long-term cooling trend, which ended late in the nineteenth century. At multi-decadal to centennial scales, temperature variability shows distinctly different regional patterns, with more similarity within each hemisphere than between them. There were no globally synchronous multi-decadal warm or cold intervals that define a worldwide Medieval Warm Period or Little Ice Age, but all reconstructions show generally cold conditions between ad 1580 and 1880, punctuated in some regions by warm decades during the eighteenth century. The transition to these colder conditions occurred earlier in the Arctic, Europe and Asia than in North America or the Southern Hemisphere regions. Recent warming reversed the long-term cooling; during the period ad 1971–2000, the area-weighted average reconstructed temperature was higher than any other time in nearly 1,400 years.},
-author = {Ahmed, Moinuddin and Anchukaitis, Kevin J. and Asrat, Asfawossen and Borgaonkar, Hemant P. and Braida, Martina and Buckley, Brendan M. and B{\"{u}}ntgen, Ulf and Chase, Brian M. and Christie, Duncan A. and Cook, Edward R. and Curran, Mark A. J. and D{\'{i}}az, Henry F. and Esper, Jan and Fan, Ze-Xin and Gaire, Narayan P. and Ge, Quansheng and Gergis, Jo{\"{e}}lle and Gonz{\'{a}}lez-Rouco, J. Fidel and Goosse, Hugues and Grab, Stefan W. and Graham, Nicholas and Graham, Rochelle and Grosjean, Martin and Hanhij{\"{a}}rvi, Sami T. and Kaufman, Darrell S. and Kiefer, Thorsten and Kimura, Katsuhiko and Korhola, Atte A. and Krusic, Paul J. and Lara, Antonio and L{\'{e}}zine, Anne-Marie and Ljungqvist, Fredrik C. and Lorrey, Andrew M. and Luterbacher, J{\"{u}}rg and Masson-Delmotte, Val{\'{e}}rie and McCarroll, Danny and McConnell, Joseph R. and McKay, Nicholas P. and Morales, Mariano S. and Moy, Andrew D. and Mulvaney, Robert and Mundo, Ignacio A. and Nakatsuka, Takeshi and Nash, David J. and Neukom, Raphael and Nicholson, Sharon E. and Oerter, Hans and Palmer, Jonathan G. and Phipps, Steven J. and Prieto, Maria R. and Rivera, Andres and Sano, Masaki and Severi, Mirko and Shanahan, Timothy M. and Shao, Xuemei and Shi, Feng and Sigl, Michael and Smerdon, Jason E. and Solomina, Olga N. and Steig, Eric J. and Stenni, Barbara and Thamban, Meloth and Trouet, Valerie and Turney, Chris S. M. and Umer, Mohammed and van Ommen, Tas and Verschuren, Dirk and Viau, Andre E. and Villalba, Ricardo and Vinther, Bo M. and von Gunten, Lucien and Wagner, Sebastian and Wahl, Eugene R. and Wanner, Heinz and Werner, Johannes P. and White, James W. C. and Yasue, Koh and Zorita, Eduardo},
-doi = {10.1038/ngeo1797},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ahmed et al. - 2013 - Continental-scale temperature variability during the past two millennia.pdf:pdf},
-journal = {Nature Geoscience},
-number = {5},
-pages = {339--346},
-title = {{Continental-scale temperature variability during the past two millennia}},
-url = {http://www.nature.com/ngeo/journal/v6/n5/full/ngeo1797.html},
-volume = {6},
-year = {2013}
-}
-@article{Preston1962,
-annote = {ArticleType: research-article / Full publication date: Apr., 1962 / Copyright {\^{A}}{\textcopyright} 1962 Ecological Society of America},
-author = {Preston, F. W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Preston - 1962 - The Canonical Distribution of Commonness and Rarity Part I.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {185--215},
-title = {{The Canonical Distribution of Commonness and Rarity: Part I}},
-url = {http://www.jstor.org/stable/1931976},
-volume = {43},
-year = {1962}
-}
-@article{Donvard1982,
-abstract = {Recent research into spatial competition suggests that the long-standing methodological convention of abstracting from space when constructing neo-classical models of competition is unsatisfactory as it materially affects the properties of such models. This paper reviews recent developments in the analysis of price discrimination and entry-deterrence within a spatial dimension. Both areas have been the scene of active research which has provided results very different from those given by neoclassical models without a spatial dimension. The implications of these developments for industrial economic analysis are discussed, particularly from the perspectives of economic welfare and public policy towards price regulation and monopoly.},
-author = {Donvard, Neil},
-doi = {10.2307/2098009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Donvard - 1982 - Recent Developments in the Analysis of Spatial Competition and their Implications for Industrial Economics.pdf:pdf},
-journal = {Journal of Industrial Economics},
-number = {1/2},
-pages = {131--151},
-title = {{Recent Developments in the Analysis of Spatial Competition and their Implications for Industrial Economics}},
-url = {https://www.jstor.org/stable/2098009},
-volume = {31},
-year = {1982}
-}
-@phdthesis{DurrieudeMadron1993,
-author = {{Durrieu de Madron}, L.},
-publisher = {ENGREF},
-title = {{Mortalit{\'{e}}, chablis et r{\^{o}}le des trou{\'{e}}es dans la sylvigen{\`{e}}se avant et apr{\`{e}}s exploitation sur le dispositif d'{\'{e}}tude sylvicole de Paracou-Guyane fran{\c{c}}aise}},
-year = {1993}
-}
-@article{Bordenave2011,
-abstract = {Within the framework of a flora and vegetation study carried out in the Bakhuis Mountains in Suriname, South America, descriptors of plant species and habitat biodiversity were used to set local-scale botanical conservation priorities. Species' diversity and habitat heterogeneity indices, relative scarcity, fragility indices for habitats and ratios of species of concern, such as rare, endemic or subendemic taxa, were processed through a multi-criteria analysis to determine a conservation priority index. One of the main objectives of the study was the setting of defensible conservation priorities at a local and regional scale. Results are discussed, with a focus on land use planning and biodiversity conservation in one of the three major evergreen rainforest regions in the world. Among the 13 vegetation types described in the study perimeter, two that were restricted in area were considered to be of higher concern for wildlife conservation: meso-xeric dwarf thickets found on latero-bauxitic hardcap hilltops, with a distinctive floristic composition, and Buxus citrifolia mesic forest patches, described for the first time in Suriname. (C) 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 94-130.},
-author = {Bordenave, Bruno Georges and {De Granville}, Jean-Jacques and Steyn, Kate},
-doi = {10.1111/j.1095-8339.2011.01163.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bordenave, De Granville, Steyn - 2011 - Quantitative botanical diversity descriptors to set conservation priorities in Bakhuis Mountains.pdf:pdf},
-journal = {Botanical Journal of the Linnean Society},
-number = {1},
-pages = {94--130},
-title = {{Quantitative botanical diversity descriptors to set conservation priorities in Bakhuis Mountains rainforest, Suriname}},
-volume = {167},
-year = {2011}
-}
-@article{Sicuro2015,
-abstract = {We propose a unifying picture where the notion of generalized entropy is related to information theory by means of a group-theoretical approach. The group structure comes from the requirement that an entropy be well defined with respect to the composition of independent systems, in the context of a recently proposed generalization of the Shannon-Khinchin axioms. We associate a general information functional to each member of a large class of non-extensive entropies, satisfying the additivity property on a set of independent systems on the basis of the underlying group law. At the same time, we also show that the Einstein likelihood function naturally emerges as a byproduct of our informational interpretation of nonadditive entropies. These results confirm the adequacy of composable entropies both in physical and social science contexts.},
-archivePrefix = {arXiv},
-arxivId = {1512.00089},
-author = {Sicuro, Gabriele and Tempesta, Piergiulio},
-eprint = {1512.00089},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sicuro, Tempesta - 2015 - Groups, Information Theory and Einstein's Likelihood Principle.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Groups, Information Theory and Einstein's Likelihood Principle}},
-url = {http://arxiv.org/abs/1512.00089},
-volume = {1512.00089},
-year = {2015}
-}
-@incollection{Feser2002b,
-address = {New York},
-author = {Feser, Edward J. and Sweeney, Stuart H.},
-booktitle = {Global Competition and Local Networks},
-editor = {McNaughton, R and Green, M},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser, Sweeney - 2002 - Spatially Binding Linkages in Manufacturing Product Chains.pdf:pdf},
-pages = {111--129},
-publisher = {Ashgate},
-title = {{Spatially Binding Linkages in Manufacturing Product Chains}},
-url = {https://www.escholar.manchester.ac.uk/uk-ac-man-scw:139077},
-year = {2002}
-}
-@article{Sabatier1985,
-abstract = {The phenology of flowering and fruiting of trees was studied from June 1980 to the end of March 1982 in the lowland rain forest of Piste Saint Elie, French Guiana. All flowering and fruiting trees over 2 cm DBH overhanging a trail 1 000 to 1 500 m long and 1 m wide were noted every second week, and all flowers and fruits which fell on the trail were collected and weighed. The following results were obtained : Fertility was always low, less than 50 {\%} of the trees over 45 cm DBH bearing fruit during the two yearly cycles. Fertility also varied from one year to the next, being higher during the second yearly cycle. However, some trees which flowered normally never bore fruit. Most tree species (from 76 to 80 {\%}, depending on the year) flowered during the « dry » season and bore fruit during the rainy season (86 to 88 {\%}). The seeds of most of the species (56 {\%}) germinated in less than one month in experimental conditions, and 22,2 {\%} in more than 4 months. Seasonality in reproduction occured in all species of dicotyle donous trees, whatever their size or age (from 2 to {\textgreater} 60 cm DBH). It was far less marked in understorey trees, epiphytes and woody lianas. Seasonality in fruiting was particularly marked among species bearing fleshy fruits disseminated by animals, although some were produced at any time of the year. Seasonality was also marked among wind-dispersed and autochorous tree species. Among trees bearing fleshy fruits, those with the larger seeds were much more seasonal than those with smaller seeds. Finally, the species which were moderately abundant on the sampling transect were more seasonal than both the scarcer and the most abundant ones. Mast fruiting was observed in 8 spe cies of Eschweilera and Lecythis (Lecythidaceae). In the rain forest studied, the fruiting peak mostly results, at the species level, from the adjustment of the maturation period to the flowering time. Biotic factors undoubtedly play an important role in determining fruiting peaks at the community level.},
-author = {Sabatier, Daniel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sabatier - 1985 - Saisonnalit{\'{e}} et d{\'{e}}terminisme du pic de fructification en for{\^{e}}t guyanaise.pdf:pdf},
-journal = {Revue d'Ecologie (La Terre et la Vie)},
-pages = {289--320},
-title = {{Saisonnalit{\'{e}} et d{\'{e}}terminisme du pic de fructification en for{\^{e}}t guyanaise}},
-url = {http://documents.irevues.inist.fr/handle/2042/55214},
-volume = {40},
-year = {1985}
-}
-@article{Ricotta2009,
-abstract = {Many applications of diversity indices are only valid if they are first transformed into their equivalent number of species. These equivalent numbers of species can be multiplicatively partitioned into independent alpha, beta and gamma components, and can be formed into mathematically consistent similarity measures. The utility of beta diversity and similarity measures that incorporate information about the degree of ecological dissimilarity between species is becoming increasingly recognized. The concept of equivalent number of species is here extended to Rao's quadratic entropy, opening the way to methods of diversity partitioning that take into account taxonomic or ecological differences between species.},
-annote = {Cited By (since 1996):25
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: TLPBA
-PubMed ID: 19818799
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; University of Rome La Sapienza, Department of Plant Biology, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo and Szeidl, Laszlo},
-doi = {10.1016/j.tpb.2009.10.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Szeidl - 2009 - Diversity partitioning of Rao's quadratic entropy.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {4},
-pages = {299--302},
-title = {{Diversity partitioning of Rao's quadratic entropy}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-70449528633{\&}partnerID=40{\&}md5=5152273c0b96c81e2152ddfb71184c48},
-volume = {76},
-year = {2009}
-}
-@article{Nei1972,
-abstract = {A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.},
-author = {Nei, Masatoshi},
-doi = {10.2307/2459777},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nei - 1972 - Genetic Distance between Populations.pdf:pdf},
-journal = {The American Naturalist},
-number = {949},
-pages = {283--292},
-title = {{Genetic Distance between Populations}},
-url = {http://www.jstor.org/stable/2459777},
-volume = {106},
-year = {1972}
-}
-@article{Wright2002,
-abstract = {Across species, leaf lifespan (LL) tends to be correlated with leaf mass per area (LMA). Previously we found that Australian perennial species from low-rainfall sites had c. 40{\%} shorter LL at a given LMA than high-rainfall species. Here we relate indices of leaf strength (work to shear, W-shear , and tissue toughness) to LL and LMA across the same suite of species. W-shear is the work required to cut a leaf with a blade; W-shear divided by leaf thickness gives tissue toughness. Low- and high-rainfall species did not differ in their LL at a given W-shear, but dry-site species had lower W-shear at a given LMA, leading to the observed LL - LMA shift with rainfall. These patterns were driven by 50{\%} lower tissue toughness in dry-site species. The lower toughness was linked with high leaf N concentration, which is known to enhance water conservation during photosynthesis in low-rainfall species. Our results suggest that a significant cost of this strategy is reduced LL for a given investment in leaf tissue (LMA).},
-author = {Wright, Ian J. and Westoby, Mark},
-doi = {10.1046/j.1469-8137.2002.00479.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright, Westoby - 2002 - Leaves at low versus high rainfall coordination of structure, lifespan and physiology.pdf:pdf},
-journal = {New Phytologist},
-number = {3},
-pages = {403--416},
-title = {{Leaves at low versus high rainfall: coordination of structure, lifespan and physiology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1469-8137.2002.00479.x/abstract},
-volume = {155},
-year = {2002}
-}
-@article{He2000,
-abstract = {1 We mapped the locations of live and dead trees in a large forest plot dominated by pioneer Douglas fir (Pseudotsuga menziesii) with an understorey of the invading late-successional species western hemlock (Tsuga heterophylla) and western red cedar (Thuja plicata) on Vancouver Island, British Columbia, Canada, to test for intra- and interspecific density-dependent effects on tree survival. 2 We analysed both the spatial patterning of trees in the plot and the relationships between neighbourhood density and tree survival. We also examined the effects of additional variables (principally elevation) as covariates in our neighbourhood analyses, 3 Both the spatial and initial neighbourhood analyses suggested strong intra- and interspecific density-dependent effects on tree survival, Douglas fir survival was significantly higher in less dense patches of conspecifics and non-random tree death led to regularly spaced survivors, as expected from intraspecific competition. The significantly lower survival of western hemlock in denser patches of Douglas fir and the resulting negative spatial association between surviving trees of these two species were consistent with interspecific competition. 4 However, having controlled for the influence of elevation on tree survival (probably mediated by variation in soil moisture) in neighbourhood analyses, although the survival of the pioneer Douglas fir trees was still subject to strong density-dependent effects., variation in its density in the overstorey no longer appeared to influence the survival of the invading late-successional species, There was, however, evidence for asymmetric interspecific density dependence between the two late-successional species since western hemlock mortality tended to be higher in denser patches of western red cedar. 5 Our results emphasize the importance of considering confounding factors in studies that seek evidence for density dependence.},
-annote = {Article
-English
-J ECOL
-347QT},
-author = {He, FangLiang and Duncan, Richard P.},
-doi = {10.1046/j.1365-2745.2000.00482.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/He, Duncan - 2000 - Density-dependent effects on tree survival in an old-growth Douglas fir forest.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {676--688},
-title = {{Density-dependent effects on tree survival in an old-growth Douglas fir forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2745.2000.00482.x/abstract},
-volume = {88},
-year = {2000}
-}
-@article{Grith2000,
-abstract = {The Moran Coe½cient spatial autocorrelation index can be decom-posed into orthogonal map pattern components. This decomposition relates it directly to standard linear regression, in which corresponding eigenvectors can be used as predictors. This paper reports comparative results between these linear regressions and their auto-Gaussian counterparts for the following georeferenced data sets: Columbus (Ohio) crime, Ottawa-Hull median family income, Toronto population density, southwest Ohio unemployment, Syra-cuse pediatric lead poisoning, and Glasgow standard mortality rates, and a small remotely sensed image of the High Peak district. This methodology is extended to auto-logistic and auto-Poisson situations, with selected data analyses including percentage of urban population across Puerto Rico, and the frequency of SIDs cases across North Carolina. These data analytic results suggest that this approach to georeferenced data analysis o¨ers considerable promise.},
-author = {Griffith, Daniel A.},
-doi = {10.1007/PL00011451},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Griffith - 2000 - A linear regression solution to the spatial autocorrelation problem.pdf:pdf},
-journal = {Journal of Geographical Systems},
-pages = {141--156},
-title = {{A linear regression solution to the spatial autocorrelation problem}},
-volume = {2},
-year = {2000}
-}
-@article{Elith2011,
-abstract = {MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.},
-author = {Elith, Jane and Phillips, Steven J. and Hastie, Trevor and Dud{\'{i}}k, Miroslav and Chee, Yung En and Yates, Colin J.},
-doi = {10.1111/j.1472-4642.2010.00725.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Elith et al. - 2011 - A statistical explanation of MaxEnt for ecologists.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {1},
-pages = {43--57},
-title = {{A statistical explanation of MaxEnt for ecologists}},
-url = {http://dx.doi.org/10.1111/j.1472-4642.2010.00725.x},
-volume = {17},
-year = {2011}
-}
-@book{Fischer2010,
-abstract = {Spatial data are an important source of scientific information. The development of high capacity and fast desk and laptop computers and the concomitant creation of geographic information systems has made it possible to explore georeferenced or mapped data as never before. This Handbook summarizes, explains, and demonstrates the nature of current models, methods, and techniques particularly designed for the analysis of spatial data. The book is designed to be a desk reference for all researchers just getting into the field of spatial data analysis as well as for seasoned spatial analysts. Relevant references are given whenever possible to direct researchers to the most useful writings on the subject. Unlike most compendia of this nature, the book starts out by exploring the available software for spatial analysis. We focus on the tools that make analysis possible. The volume then describes briefly but clearly the many techniques embodied in the fields of exploratory spatial data analysis, spatial statistics, geostatistics, and spatial econometrics. In addition, attention is given to the methods used for the analysis of remotely sensed data. Finally, a number of example sections are included that demonstrate the application of spatial analysis in the economic, environmental, and health sciences. The wide range of approaches described helps readers better understand their data and the techniques needed for spatial analysis. The volume features contributions from the very best scholars in the field. Their explanations are able to communicate the fundamental ideas of their subject area succinctly and accessibly.},
-editor = {Fischer, Manfred M. and Getis, Arthur},
-isbn = {9783642036460},
-publisher = {Springer},
-title = {{Handbook of Applied Spatial Analysis}},
-url = {http://www.springer.com/la/book/9783642036460},
-year = {2010}
-}
-@article{Pavoine2017,
-abstract = {A new index of species' functional originality is presented and evaluated. The properties of this index and a range of published indices are analyzed. Phylogenetic originality can rarely serve as a proxy for functional originality Transforming functional data into functional trees modifies species' originalities. Indices are extended to originality at all scales from populations to regions.},
-author = {Pavoine, Sandrine and Bonsall, Michael B. and Dupaix, Ama{\"{e}}l and Jacob, Ute and Ricotta, Carlo},
-doi = {10.1016/j.ecolind.2017.06.056},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2017 - From phylogenetic to functional originality Guide through indices and new developments.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {196--205},
-title = {{From phylogenetic to functional originality : Guide through indices and new developments}},
-url = {http://dx.doi.org/10.1016/j.ecolind.2017.06.056},
-volume = {82},
-year = {2017}
-}
-@article{Anderson2006a,
-abstract = {The traditional likelihood-based test for differences in multivariate dispersions is known to be sensitive to nonnormality. It is also impossible to use when the number of variables exceeds the number of observations. Many biological and ecological data sets have many variables, are highly skewed, and are zero-inflated. The traditional test and even some more robust alternatives are also unreasonable in many contexts where measures of dispersion based on a non-Euclidean dissimilarity would be more appropriate. Distance-based tests of homogeneity of multivariate dispersions, which can be based on any dissimilarity measure of choice, are proposed here. They rely on the rotational invariance of either the multivariate centroid or the spatial median to obtain measures of spread using principal coordinate axes. The tests are straightforward multivariate extensions of Levene's test, with P-values obtained either using the traditional F-distribution or using permutation of either least-squares or LAD residuals. Examples illustrate the utility of the approach, including the analysis of stabilizing selection in sparrows, biodiversity of New Zealand fish assemblages, and the response of Indonesian reef corals to an El Ni{\~{n}}o. Monte Carlo simulations from the real data sets show that the distance-based tests are robust and powerful for relevant alternative hypotheses of real differences in spread.},
-author = {Anderson, Marti J.},
-doi = {10.1111/j.1541-0420.2005.00440.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anderson - 2006 - Distance-based tests for homogeneity of multivariate dispersions.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {245--53},
-title = {{Distance-based tests for homogeneity of multivariate dispersions.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/16542252},
-volume = {62},
-year = {2006}
-}
-@article{Diniz-Filho2011,
-abstract = {1. Although species richness is the most common metric for biodiversity, it is important to consider that among-species differences matter for many important processes such as ecosystem functioning and assembly patterns. Thus, alternative metrics have been proposed to measure phylogenetic (PD) and functional diversity (FD). 2. Here, we analysed the correlation structure and the geographic patterns of different phylogenetic and functional diversity metrics using 1000 Carnivora (mammals) assemblages distributed world-wide. We also proposed a general approach to estimate these metrics based on phylogenetic eigenvector regressions. 3. We showed that the cumulative variance of phylogenetic eigenvectors within assemblages converges to one metric of phylogenetic clustering, the phylogenetic species variability (PSV), which was recently proposed in the literature. Phylogenetic eigenvectors have also been used to model trait variation (i.e. body mass); therefore, the same reasoning allows us to decouple trait diversity (i.e. body mass) into phylogenetic FD(P) and specific FD(S) components. The cumulative variance of these components within assemblages, for a single trait or multiple traits, offers a direct estimate of the evolutionary and ecological components of functional variation. Our results indicated that the variance of the phylogenetic component of body mass FD(P) estimated within assemblages was highly correlated with a common measure of functional diversity (Raos Q). 4. Our general approach based on phylogenetic eigenvectors provides similar results when compared to other metrics of FD and PD, but also has some important advantages. First, it allows a direct interpretation of at which hierarchical level in the phylogeny (expressed by different sets of eigenvectors) the patterns in PD and FD appear. Secondly, phylogenetic components of FD can be analysed directly because of the partition of functional diversity into FD(P) and FD(S), so it eliminates the need to generate a posteriori phylogenetic correlations between PD and FD based on independently derived metrics, as well as of these metrics with other components of environmental variation.},
-author = {Diniz-Filho, Jos{\'{e}} Alexandre F. and Cianciaruso, Marcus Vinicius and Rangel, Thiago Fernando and Bini, Luis Mauricio},
-doi = {10.1111/j.1365-2435.2011.01836.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diniz-Filho et al. - 2011 - Eigenvector estimation of phylogenetic and functional diversity.pdf:pdf},
-journal = {Functional Ecology},
-number = {4},
-pages = {735--744},
-title = {{Eigenvector estimation of phylogenetic and functional diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2011.01836.x/abstract},
-volume = {25},
-year = {2011}
-}
-@article{Dungan2002,
-abstract = {Concepts of spatial scale, such as extent, grain, resolution, range, footprint, support and cartographic ratio are not interchangeable. Because of the potential confusion among the definitions of these terms, we suggest that authors avoid the term "scale" and instead refer to specific concepts. In particular, we are careful to discriminate between observation scales, scales of ecological phenomena and scales used in spatial statistical analysis. When scales of observation or analysis change, that is, when the unit size, shape, spacing or extent are altered, statistical results are expected to change. The kinds of results that may change include estimates of the population mean and variance, the strength and character of spatial autocorrelation and spatial anisotropy, patch and gap sizes and multivariate relationships. The first three of these results (precision of the mean, variance and spatial autocorrelation) can sometimes be estimated using geostatistical support-effect models. We present four case studies of organism abundance and cover illustrating some of these changes and how conclusions about ecological phenomena (process and structure) may be affected. We identify the influence of observational scale on statistical results as a subset of what geographers call the Modifiable Area Unit Problem (MAUP). The way to avoid the MAUP is by careful construction of sampling design and analysis. We recommend a set of considerations for sampling design to allow useful tests for specific scales of a phenomenon under study. We further recommend that ecological studies completely report all components of observation and analysis scales to increase the possibility of cross-study comparisons.},
-author = {Dungan, J. L. and Perry, Joe N. and Dale, Mark R.T. and Legendre, Pierre and Citron-Pousty, Steven and Fortin, Marie-Jos{\'{e}}e and Jakomulska, A. and Miriti, M. and Rosenberg, Michael S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dungan et al. - 2002 - A Balanced View of Scale in Spatial Statistical Analysis.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {626--640},
-title = {{A Balanced View of Scale in Spatial Statistical Analysis}},
-url = {http://www.jstor.org/stable/3683665},
-volume = {25},
-year = {2002}
-}
-@book{Casetta2014,
-address = {Paris},
-editor = {Casetta, Elena and Delord, Julien},
-isbn = {978-2-919694-54-9},
-publisher = {Editions Mat{\'{e}}riologiques},
-title = {{La biodiversit{\'{e}} en question. Enjeux philosophiques, {\'{e}}thiques et scientifiques}},
-year = {2014}
-}
-@article{Das2004,
-abstract = {A vector of forest variability consisting of a forest stand diversity index and a compactness index has been defined. Forest stand diversity depends on the unevenness of the forest that is characterized as a continuum from an even-aged forest with only one patch to an uneven-aged forest with infinite number of patches. A forest stand diversity index is proposed to quantify the point at which a forest falls on this continuum. The shape and fragmentation of a forest is expressed in a compactness index. Forest stand diversity and compactness both affect the potential of a forest to support wildlife. Analytical relationships among the compactness index, home range size relative to the forest area, and the wildlife population has been postulated. These indices can be used for valuation of forest diversity and for developing sustainable forest management plans. D},
-author = {Das, Jitendra Kumar and Nautiyal, Jagdish},
-doi = {10.1016/j.forpol.2004.03.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Das, Nautiyal - 2004 - Forest variability index a vector quantifying forest stand diversity and forest compactness.pdf:pdf},
-journal = {Forest Policy and Economics},
-number = {3-4},
-pages = {271--288},
-title = {{Forest variability index: a vector quantifying forest stand diversity and forest compactness}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1389934104000279},
-volume = {6},
-year = {2004}
-}
-@phdthesis{Cabrera-Gaillard1989,
-address = {Montpellier},
-author = {Cabrera-Gaillard, Claudio},
-pages = {66 p},
-publisher = {Ecole Sup{\'{e}}rieure d'Agronomie Tropicale},
-title = {{Analyse de la r{\'{e}}partition spatiale des arbres en for{\^{e}}t dense guyanaise}},
-year = {1989}
-}
-@article{Gleason1922,
-annote = {ArticleType: research-article / Full publication date: Apr., 1922 /},
-author = {Gleason, Henry Allan},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gleason - 1922 - On the Relation Between Species and Area.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {158--162},
-title = {{On the Relation Between Species and Area}},
-url = {http://www.jstor.org/stable/1929150},
-volume = {3},
-year = {1922}
-}
-@article{Bell2001,
-abstract = {The central themes of community ecology—distribution, abundance, and diversity— display strongly marked and very general patterns. These include the log-normal distribution of abundance, the relation between range and abundance, the species- area law, and the turnover of species composition. Each pattern is the subject of a large literature that interprets it in terms of ecological processes, typically involving the sorting of differently specialized species onto heterogeneous landscapes. All of these patterns can be shown to arise, however, from neutral community models in which all individuals have identical properties, as the consequence of local dispersal alone. This implies, at the least, that functional interpretations of these patterns must be reevaluated. More fundamentally, neutral community models provide a general theory for biodiversity and conservation biology capable of predicting the fundamen- tal processes and patterns of community ecology. T},
-author = {Bell, Graham},
-doi = {10.1126/science.293.5539.2413},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bell - 2001 - Neutral Macroecology.pdf:pdf},
-journal = {Science},
-pages = {2413--2419},
-title = {{Neutral Macroecology}},
-volume = {293},
-year = {2001}
-}
-@misc{Ritter2017,
-abstract = {Environmental Impact Assessment (EIA) has the goal of providing decision makers with an indication of the likely environmental consequences of planned actions risking environmental changes and, when necessary, allowing revision of these actions to mitigate adverse impacts. Here we provide an overview of the efficiency of EIA with emphasis on Brazilian Amazonia and discuss the problems and challenges with this type of assessment in highly diverse ecosystems. We concentrate on the methodology and performance of EIAs for three of the most recent and largest infrastructure projects in Amazonia: the Belo Monte hydroelectric dam, the BR-319 Highway, and the Juruti bauxite mine. We conclude that all of these EIAs fall short of properly assessing the expected impact of infrastructure development in situ, and that their results had little or no effect on policy decisions. To improve the reliability and usefulness of EIAs in biologically diverse ecosystems, we suggest three relatively fast and cost-effective complementary approaches for assessing biodiversity: remote sensing, reflectance spectroscopy, and DNA meta-barcoding. We discuss how these emerging cutting-edge techniques can help in identifying environmental threats and the consequences of different activities in Amazonia. The ability to monitor the state of the environment and the likely impacts of human activities on natural resources is fundamental to evidence-based decisions on development choices, to the design of appropriate management strategies, and to mitigate biological and ecological consequences.},
-author = {Ritter, Camila D. and McCrate, Gabriel and Nilsson, R. Henrik and Fearnside, Philip M. and Palme, Ulrika and Antonelli, Alexandre},
-booktitle = {Biological Conservation},
-doi = {10.1016/j.biocon.2016.12.031},
-pages = {161--168},
-title = {{Environmental impact assessment in Brazilian Amazonia: Challenges and prospects to assess biodiversity}},
-volume = {206},
-year = {2017}
-}
-@article{Couteron1997,
-abstract = {Spatial patterns of woody individuals were studied in a semi-arid savanna of West Africa located in Burkina Faso at and around 14° 12′ N and 2° 27′ W. The study was based upon a 10.24 ha plot within which individuals were mapped. Spatial pattern analysis was carried out using second order characteristics of point processes as K functions and pair correlations. The overall density amounted to 298 individuals ha-1. The most abundant species were Combretum micranthum G. Don., Grewia bicolor Juss. and Pterocarpus lucens Lepr. Anogeissus leiocarpus (D.C.) G. et Perr. was also an important constituant of this vegetation type, owing to its taller stature. Clumped spatial distributions were identified for all species except for two, for which complete spatial randomness (CSR) was found (including P. lucens, a dominant woody plant). No regular pattern was found even when tall individuals were considered alone. Aggregation dominates interspecific relationships, resulting in multispecific clumps and patches. The overall aggregation pattern was constituted by two different structures. A coarse-grain pattern of ca. 30–40 m was based on edaphic features, and expresses the contrast between sparse stands on petroferric outcrops and denser patches on less shallow soils. A finer-grain pattern made of clumps ca. 5–10 m wide, with no obvious relation to pre-existing soil heterogeneity. There was no overall pattern for saplings (between 0.5 m and 1.5 m in height) irrespective of species, and thus no obvious common facilitation factor. For species with a high recruitment level there was no significant relationship between mature adult and saplings. The only case of clumped saplings with randomly distributed adults was found in P. lucens. However, this cannot be unequivocally interpreted as density dependent regulation since the existence of such a process was not consistent with the spatial distribution of dead P. lucens individuals (victims of the last drought). The mean density around dead P. lucens was lower than around surviving ones, indicating that the last drought tended to reinforce clumping rather than promote a regular pattern of trees. Spatial pattern analysis yielded no evidence supporting a hypothesis of stand density regulation through competition between individuals. Other processes, as surface sealing of bare soils or insufficient recruitment, may play a more important role in preventing a savanna-like vegetation from turning into denser woodlands or thickets.},
-author = {Couteron, Pierre and Kokou, Kouami},
-doi = {10.1023/A:1009723906370},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Couteron, Kokou - 1997 - Woody vegetation spatial patterns in a semi-arid savana of Burkina Faso, West Africa.pdf:pdf},
-journal = {Plant Ecology},
-pages = {211--227},
-title = {{Woody vegetation spatial patterns in a semi-arid savana of Burkina Faso, West Africa}},
-url = {http://link.springer.com/article/10.1023/A:1009723906370},
-volume = {132},
-year = {1997}
-}
-@article{Pallmann2012,
-abstract = {Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these ‘raw' indices can be corrected by transforming them into ‘true' diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of ‘true' diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package ‘simboot'.},
-author = {Pallmann, Philip and Schaarschmidt, Frank and Hothorn, Ludwig A. and Fischer, Christiane and Nacke, Heiko and Priesnitz, Kai U. and Schork, Nicholas J.},
-doi = {10.1111/1755-0998.12004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pallmann et al. - 2012 - Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity ind.pdf:pdf},
-journal = {Molecular Ecology Resources},
-number = {6},
-pages = {1068--1078},
-title = {{Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices}},
-url = {http://dx.doi.org/10.1111/1755-0998.12004},
-volume = {12},
-year = {2012}
-}
-@article{Chiu2014,
-abstract = {Until now, decomposition of abundance-sensitive gamma (regional) phylogenetic diversity measures into alpha and beta (within- and between-group) components has been based on an additive partitioning of phylogenetic generalized entropies, especially Rao's quadratic entropy. This additive approach led to a phylogenetic measure of differentiation between assemblages: (gamma alpha)/gamma. We show both empirically and theoretically that this approach inherits all of the problems recently identified in the additive partitioning of non-phylogenetic generalized entropies. When within-assemblage (alpha) quadratic entropy is high, the additive beta and the differentiation measure (gammaalpha)/gamma always tend to zero (implying no differentiation) regardless of phylogenetic structures and differences in species abundances across assemblages. Likewise, the differentiation measure based on the phylogenetic generalization of Shannon entropy always approaches zero whenever gamma phylogenetic entropy is high. Such critical flaws, inherited from their non-phylogenetic parent measures (Gini-Simpson index and Shannon entropy respectively), have caused interpretational problems. These flaws arise because phylogenetic generalized entropies do not obey the replication principle, which ensures that the diversity measures are linear with respect to species addition or group pooling. Furthermore, their complete partitioning into independent components is not additive (except for phylogenetic entropy). Just as in the non-phylogenetic case, these interpretational problems are resolved by using phylogenetic Hill numbers that obey the replication principle. Here we show how to partition the phylogenetic gamma diversity based on Hill numbers into independent alpha and beta components, which turn out to be multiplicative. The resulting phylogenetic beta diversity (ratio of gamma to alpha) measures the effective number of completely phylogenetically distinct assemblages. This beta component measures pure differentiation among assemblages and thus can be used to construct several classes of similarity or differentiation measures normalized onto the range [0, 1]. We also propose a normalization to fix the traditional additive phylogenetic similarity and differentiation measures, and we show that this yields the same similarity and differentiation measures we derived from multiplicative phylogenetic diversity partitioning. We thus can achieve a consensus on phylogenetic similarity and differentiation measures, including N-assemblage phylogenetic generalizations of the classic Jaccard, S{\o}rensen, Horn, and Morisita-Horn measures. Hypothetical and real examples are used for illustration.},
-annote = {Cited By (since 1996):1
-Export Date: 25 February 2014
-Source: Scopus},
-author = {Chiu, Chun-Huo and Jost, Lou and Chao, Anne},
-doi = {10.1890/12-0960.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu, Jost, Chao - 2014 - Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers.pdf:pdf},
-journal = {Ecological Monographs},
-number = {1},
-pages = {21--44},
-title = {{Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893294439{\&}partnerID=40{\&}md5=c8c12fa4372cf22dd4a885fb019f7868},
-volume = {84},
-year = {2014}
-}
-@article{Isaac2007,
-abstract = {Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species) do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.},
-author = {Isaac, Nick J.B. and Turvey, Samuel T. and Collen, Ben and Waterman, Carly and Baillie, Jonathan E.M.},
-doi = {10.1371/journal.pone.0000296},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Isaac et al. - 2007 - Mammals on the EDGE Conservation Priorities Based on Threat and Phylogeny.pdf:pdf},
-issn = {1932-6203},
-journal = {PLoS ONE},
-number = {3},
-pages = {e296},
-title = {{Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny}},
-url = {http://dx.plos.org/10.1371/journal.pone.0000296},
-volume = {2},
-year = {2007}
-}
-@article{Guan2009,
-abstract = {We introduce two new variance estimation procedures that use non-overlapping and overlapping blocks, respectively. The non-overlapping blocks estimator can be viewed as the limit of the thinned block bootstrap estimator recently proposed in Guan Loh (2007), by letting the number of thinned processes and bootstrap samples therein both increase to infinity. The non-overlapping blocks estimator can be obtained quickly since it does not require any thinning or bootstrap steps, and it is more stable. The overlapping blocks estimator further improves the performance of the non-overlapping blocks with a modest increase in computation time. A simulation study demonstrates the superiority of the proposed estimators over the thinned block bootstrap estimator. {\textcopyright} 2009 Biometrika Trust.},
-annote = {cited By (since 1996) 4},
-author = {Guan, Yontao},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2009 - Fast block variance estimation procedures for inhomogeneous spatial point processes.pdf:pdf},
-isbn = {10.1093/biomet/asn072},
-journal = {Biometrika},
-number = {1},
-pages = {213--220},
-title = {{Fast block variance estimation procedures for inhomogeneous spatial point processes}},
-volume = {96},
-year = {2009}
-}
-@article{Zak2003,
-abstract = {A current debate in ecology centers on the extent to which ecosystem function depends on biodiversity. Here, we provide evidence from a long-term field manipulation of plant diversity that soil microbial communities, and the key ecosystem processes that they mediate, are significantly altered by plant species richness. After seven years of plant growth, we determined the composition and function of soil microbial communities beneath experimental plant diversity treatments containing 1-16 species. Microbial community biomass, respiration,. and fungal abundance significantly increased with greater plant diversity, as did N mineralization rates. However, changes in microbial community biomass, activity, and composition largely resulted-from the higher levels of plant production associated with greater diversity, rather than from plant diversity per se., Nonetheless, greater plant production could not explain more rapid N mineralization, indicating that plant diversity affected this microbial process, which controls. rates of ecosystem N cycling. Greater N availability probably contributed to the positive relationship between plant diversity and productivity in the N-limited soils of our experiment, suggesting that plant-microbe interactions in soil are an integral component of plant diversity's influence on ecosystem function.},
-author = {Zak, Donald R. and Holmes, William E. and White, David C. and Peacock, Aaron D. and Tilman, David},
-doi = {10.1890/02-0433},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zak et al. - 2003 - Plant diversity, soil microbial communities, and ecosystem function Are there any links.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2042--2050},
-title = {{Plant Diversity, Soil Microbial Communities, and Ecosystem Function: Are There Any Links?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/02-0433/abstract},
-volume = {84},
-year = {2003}
-}
-@article{Sharp2015,
-abstract = {Translation of the seminal 1877 paper by Ludwig Boltzmann which for the first time established the probabilistic basis of entropy. Includes a scientific commentary.},
-author = {Sharp, Kim and Matschinsky, Franz},
-doi = {10.3390/e17041971},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sharp, Matschinsky - 2015 - Translation of Ludwig Boltzmann's paper on the relationship between the second fundamental theorem of the me.pdf:pdf},
-journal = {Entropy},
-number = {4},
-pages = {1971--2009},
-title = {{Translation of Ludwig Boltzmann's paper "on the relationship between the second fundamental theorem of the mechanical theory of heat and probability calculations regarding the conditions for thermal equilibrium"}},
-url = {http://www.mdpi.com/1099-4300/17/4/1971},
-volume = {17},
-year = {2015}
-}
-@article{Bailey1971,
-abstract = {Most obiections to the use of simple discrete concentration measures note that such measures fail to take into account the number and individual sizes of firms in an industry. Proponents of the use of cumulative concentration ratios (Herfindahl, etc.) contend that if individual firm-size information were available, superior results would be obtained. In assessing the validity of these obiections, the authors find that ( 1) no one of the standard concentration indexes appears superior to any others, and (2) the number and size distribution of individual firms does not seem to affect materially the results obtained.},
-author = {Bailey, Duncan and Boyle, Stanley E.},
-doi = {10.2307/2284215},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bailey, Boyle - 1971 - The Optimal Measure of Concentration.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {336},
-pages = {702--706},
-title = {{The Optimal Measure of Concentration}},
-url = {https://www.jstor.org/stable/2284215},
-volume = {66},
-year = {1971}
-}
-@article{Ricotta2016,
-abstract = {Plot-to-plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 × 2 contingency table. However, more recently, dissimilarity measures that incorporate information about the degree of functional differences between the species in both plots have received increasing attention. This is because such “functional dissimilarity measures” capture information on the species' functional traits, which is ignored by traditional coefficients. Therefore, functional dissimilarity measures tend to correlate more strongly with ecosystem-level processes, as species influence these processes via their traits. In this study, we introduce a new family of dissimilarity measures for presence and absence data, which consider functional dissimilarities among species in the calculation of the matching/mismatching components of the 2 × 2 contingency table. Within this family, the behavior of the Jaccard coefficient, together with its additive components, species replacement, and richness difference, is examined by graphical comparisons and ordinations based on simulated data.},
-author = {Ricotta, Carlo and Podani, J{\'{a}}nos and Pavoine, Sandrine},
-doi = {10.1002/ece3.2214},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Podani, Pavoine - 2016 - A family of functional dissimilarity measures for presence and absence data.pdf:pdf},
-journal = {Ecology and Evolution},
-number = {15},
-pages = {5383--5389},
-title = {{A family of functional dissimilarity measures for presence and absence data}},
-url = {http://doi.wiley.com/10.1002/ece3.2214},
-volume = {6},
-year = {2016}
-}
-@article{Swenson2007,
-abstract = {The relative importance of biotic, abiotic, and stochastic processes in structuring ecological communities continues to be a central focus in community ecology. In order to assess the role of phylogenetic relatedness on the nature of biodiversity we first quantified the degree of phylogenetic niche conservatism of several plant traits linked to plant form and function. Next we quantified the degree of phylogenetic relatedness across two fundamental scaling dimensions: plant size and neighborhood size. The results show that phylogenetic niche conservatism is likely widespread, indicating that closely related species are more functionally similar than distantly related species. Utilizing this information we show that three of five tropical forest dynamics plots (FDPs) exhibit similar scale-dependent patterns of phylogenetic structuring using only a spatial scaling axis. When spatial- and size-scaling axes were analyzed in concert, phylogenetic overdispersion of co-occurring species was most important at small spatial scales and in four of five FDPs for the largest size class. These results suggest that phylogenetic relatedness is increasingly important: (1) at small spatial scales, where phylogenetic overdispersion is more common, and (2) in large size classes, where phylogenetic overdispersion becomes more common throughout ontogeny. Collectively, our results highlight the critical spatial and size scales at which the degree of phylogenetic relatedness between constituent species influences the structuring of tropical forest diversity.},
-author = {Swenson, Nathan G. and Enquist, Brian J. and Thompson, Jill and Zimmerman, Jess K.},
-doi = {10.1890/06-1499.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Swenson et al. - 2007 - The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1770--80},
-title = {{The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/06-1499.1/abstract},
-volume = {88},
-year = {2007}
-}
-@article{Hughes2001,
-author = {Hughes, Jennifer B. and Hellmann, Jessica J. and Ricketts, Taylor H. and Bohannan, Brendan J. M.},
-doi = {10.1128/AEM.67.10.4399},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hughes et al. - 2001 - Counting the Uncountable Statistical Approaches to Estimating Microbial Diversity.pdf:pdf},
-journal = {Applied and Environmental Microbiology},
-number = {10},
-pages = {4399--4406},
-pmid = {11571135},
-title = {{Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity}},
-volume = {67},
-year = {2001}
-}
-@article{Liu2015a,
-abstract = {Many community experiments have shown a positive relationship between plant biodiversity and community productivity, with biodiversity measured multiple ways based on taxonomy, function and phylogeny. Whether these different measures of biodiversity and their interactions explain variation in productivity in natural assemblages has rarely been tested. In a removal experiment using natural alpine assemblages in the Tibetan Plateau, we manipulated species richness and functional diversity to examine how different measures of biodiversity predict aboveground biomass production. We combined different biodiversity measures (functional, phylogenetic, richness, evenness) in generalized linear models to determine which combinations provided the most parsimonious explanations of variation in biomass production. Although multivariate functional diversity indices alone consistently explained more variation in productivity than other single measures, phylogenetic diversity and plant height represented the most parsim...},
-author = {Liu, Jiajia and Zhang, Xinxin and Song, Feifan and Zhou, Shurong and Cadotte, Marc W. and Bradshaw, Corey J. A.},
-doi = {10.1890/14-1034.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liu et al. - 2015 - Explaining maximum variation in productivity requires phylogenetic diversity and single functional traits.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {176--183},
-title = {{Explaining maximum variation in productivity requires phylogenetic diversity and single functional traits}},
-volume = {96},
-year = {2015}
-}
-@article{Chave2005,
-abstract = {Tropical forests hold large stores of carbon, yet uncertainty remains regarding their quantitative contribution to the global carbon cycle. One approach to quantifying carbon biomass stores consists in inferring changes from long-term forest inventory plots. Regression models are used to convert inventory data into an estimate of aboveground biomass (AGB). We provide a critical reassessment of the quality and the robustness of these models across tropical forest types, using a large dataset of 2,410 trees ! 5 cm. diameter, directly harvested in 27 study sites across the tropics. Proportional relationships between aboveground biomass and the product of wood density, trunk cross-sectional area, and total height are constructed. We also develop a regression model involving wood density and stem diameter only. Our models were tested for secondary and old-growth forests, for dry, moist and wet forests, for lowland and montane forests, and for mangrove forests. The most important predictors of AGB of a tree were, in decreasing order of importance, its trunk diameter, wood specific gravity, total height, and forest type (dry, moist, or wet). Overestimates prevailed, giving a bias of 0.5-6.5{\%} when errors were averaged across all stands. Our regression models can be used reliably to predict aboveground tree biomass across a broad range of tropical forests. Because they are based on an unprecedented dataset, these models should improve the quality of tropical biomass estimates, and bring consensus about the contribution of the tropical forest biome and tropical deforestation to the global carbon cycle.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Andalo, C. and Brown, Sandra and Cairns, M. A. and Chambers, Jeffrey Q. and Eamus, D. and Folster, H. and Fromard, F and Higuchi, Niro and Kira, T. and Lescure, Jean-Paul and Nelson, B. W. and Ogawa, H. and Puig, Henri and Riera, Bruno and Yamakura, T.},
-doi = {10.1007/s00442-005-0100-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave et al. - 2005 - Tree allometry and improved estimation of carbon stocks and balance in tropical forests.pdf:pdf},
-journal = {Oecologia},
-number = {1},
-pages = {87--99},
-title = {{Tree allometry and improved estimation of carbon stocks and balance in tropical forests}},
-volume = {145},
-year = {2005}
-}
-@article{Ohser1983,
-abstract = {For the reduced second moment measure of stationary point processes several estimators are presented. In order to show the most general conditions under which the estimators are applicable, some properties of non-stationary point processes are introduced making it possible to reduce the second moment measure as in the stationary case. For the stationary Poisson process variances of the estimators are given.},
-author = {Ohser, J.},
-doi = {10.1080/02331888308801687},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ohser - 1983 - On estimators for the reduced second moment measure of point processes.pdf:pdf},
-journal = {Series Statistics},
-number = {1},
-pages = {63--71},
-title = {{On estimators for the reduced second moment measure of point processes}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/02331888308801687},
-volume = {14},
-year = {1983}
-}
-@article{Lavorel2002,
-abstract = {1. The concept of plant functional type proposes that species can be grouped according to common responses to the environment and/or common effects on ecosystem processes. However, the knowledge of relationships between traits associated with the response of plants to environmental factors such as resources and disturbances (response traits), and traits that determine effects of plants on ecosystem functions (effect traits), such as biogeochemical cycling or propensity to disturbance, remains rudimentary. 2. We present a framework using concepts and results from community ecology, ecosystem ecology and evolutionary biology to provide this linkage. Ecosystem functioning is the end result of the operation of multiple environmental filters in a hierarchy of scales which, by selecting individuals with appropriate responses, result in assemblages with varying trait composition. Functional linkages and trade-offs among traits, each of which relates to one or several processes, determine whether or not filtering by different factors gives a match, and whether ecosystem effects can be easily deduced from the knowledge of the filters. 3. To illustrate this framework we analyse a set of key environmental factors and ecosystem processes. While traits associated with response to nutrient gradients strongly overlapped with those determining net primary production, little direct overlap was found between response to fire and flammability. 4. We hypothesize that these patterns reflect general trends. Responses to resource availability would be determined by traits that are also involved in biogeochemical cycling, because both these responses and effects are driven by the trade-off between acquisition and conservation. On the other hand, regeneration and demographic traits associated with response to disturbance, which are known to have little connection with adult traits involved in plant ecophysiology, would be of little relevance to ecosystem processes. 5. This framework is likely to be broadly applicable, although caution must be exercised to use trait linkages and trade-offs appropriate to the scale, environmental conditions and evolutionary context. It may direct the selection of plant functional types for vegetation models at a range of scales, and help with the design of experimental studies of relationships between plant diversity and ecosystem properties.},
-author = {Lavorel, Sandra and Garnier, Eric},
-doi = {10.1046/j.1365-2435.2002.00664.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lavorel, Garnier - 2002 - Predicting changes in community composition and ecosystem functioning from plant traits revisiting the Holy Gr.pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {545--556},
-title = {{Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2435.2002.00664.x/abstract},
-volume = {16},
-year = {2002}
-}
-@article{Baraloto2007,
-abstract = {We investigated the relationship between habitat association and physiological performance in four congeneric species pairs exhibiting contrasting distributions between seasonally flooded and terra firme habitats in lowland tropical rain forests of French Guiana, including Virola and Iryanthera (Myristicaceae), Symphonia (Clusiaceae), and Eperua (Caesalpiniaceae). We analyzed 10-year data sets of mapped and measured saplings (stems ?150 cm in height and ,10 cm diameter at breast height [dbh]) and trees (stems ?10 cm dbh) across 37.5 ha of permanent plots covering a 300-ha zone, within which seasonally flooded areas (where the water table never descends below 1 m) have been mapped. Additionally, we tested the response of growth, survival, and leaf functional traits of these species to drought and flood stress in a controlled experiment. We tested for habitat preference using a modification of the torus translation method. Strong contrasting associations of the species pairs of Iryanthera, Virola, and Symphonia were observed at the sapling stage, and these associations strengthened for the tree stage. Neither species of Eperua was significantly associated with flooded habitats at the sapling stage, but E. falcata was significantly and positively associated with flooded forests at the tree stage, and trees of E. grandiflora were found almost exclusively in nonflooded habitats. Differential performance provided limited explanatory support for the observed habitat associations, with only congeners of Iryanthera exhibiting divergent sapling survival and tree growth. Seedlings of species associated with flooded forest tended to have higher photosynthetic capacity than their congeners at field capacity. In addition, they tended to have the largest reductions in leaf gas exchange and growth rate in response to experimental drought stress and the least reductions in response to experimental inundation. The corroboration of habitat association with differences in functional traits and, to a lesser extent, measures of performance provides an explanation for the regional coexistence of these species pairs. We suggest that specialization to seasonally flooded habitats may explain patterns of adaptive radiation in many tropical tree genera and thereby provide a substantial contribution to regional tree diversity},
-author = {Baraloto, Christopher and Morneau, Fran{\c{c}}ois and Bonal, Damien and Blanc, Lilian and Ferry, Bruno},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2007 - Seasonal water stress tolerance and habitat associations within four neotropical tree genera.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {478--489},
-title = {{Seasonal water stress tolerance and habitat associations within four neotropical tree genera}},
-url = {http://www.esapubs.org/archive/ecol/E088/029/default.htm},
-volume = {88},
-year = {2007}
-}
-@article{Pavoine2005c,
-abstract = {Rao has developed quadratic entropy to measure diversity in a set of entities divided up among a fixed set of categories. This index depends on a chosen matrix of dissimilarities among categories and a frequency distribution of these categories. With certain choices of dissimilarities, this index could be maximized over all frequency distributions by eliminating several categories. This unexpected result is radically opposite to those obtained with usual diversity indices. We demonstrate that the elimination of categories to maximize the quadratic entropy depends on mathematical properties of the chosen dissimilarities. In particular, when quadratic entropy is applied to ultrametric dissimilarities, all categories are retained in order to reach its maximal value. Three examples, varying from simple one-dimensional to ultrametric dissimilarity matrices, are provided. We conclude that, as far as diversity measurement is concerned, quadratic entropy is most relevant when applied to ultrametric dissimilarities. {\&}COPY; 2005 Elsevier Inc. All rights reserved.},
-author = {Pavoine, Sandrine and Ollier, S{\'{e}}bastien and Pontier, D.},
-doi = {10.1016/j.tpb.2005.01.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Ollier, Pontier - 2005 - Measuring diversity from dissimilarities with Rao's quadratic entropy Are any dissimilarities suitable.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {4},
-pages = {231--239},
-title = {{Measuring diversity from dissimilarities with Rao's quadratic entropy: Are any dissimilarities suitable?}},
-url = {http://www.sciencedirect.com/science/article/pii/S0040580905000183},
-volume = {67},
-year = {2005}
-}
-@article{Whittaker1965,
-abstract = {Most plant communities consist of several or many species which compete for light, water, and nutrients. Species in a given community may be ranked by their relative success in competition; productivity seems to be the best measure of their success or importance in the community. Curves of decreasing productivity connect the few most iniportant species (the dominants) with a larger number of species of intermediate importance (whose number prilnarily determines the community's diversity or richness in species) and a smaller number of rare species. These curves are of varied fortns and are believed to express different patterns of competition and niche differentiation in communities. It is probably true of plants, as of animals, that no two species in a stable community occupy the same niche. Evolution of niche differentiation makes possible the occurrence together of many plant species which are partial, rather than direct, competitors. Species tend to evolve also toward habitat differentiation, toward scattering of their centers of niaximum population density in relation to environmental gradients, so that few species are competing with one another in their population centers. Evolution of both niche and habitat differentiation permits many species to exist together in com{\~{}}nunities as partial conipetitors, with distributions broadly and continuously overlapping, forming the landscape's many intergrading communities.},
-annote = {Cited By (since 1996): 280
-Export Date: 28 December 2011
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Whittaker, R.H.; Department of Biology, Brooklyn College, City University of New York, Brooklyn},
-author = {Whittaker, R. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker - 1965 - Dominance and diversity in land plant communities.pdf:pdf},
-journal = {Science},
-number = {3655},
-pages = {250--260},
-title = {{Dominance and diversity in land plant communities}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0001631420{\&}partnerID=40{\&}md5=56d0ae231a8bec2fdf6ddadf2b001c7b},
-volume = {147},
-year = {1965}
-}
-@article{BROWN1996,
-author = {Brown, Eleanor D. and Hopkins, Michael J. G.},
-doi = {10.1111/j.1442-9993.1996.tb00623.x},
-issn = {1442-9985},
-journal = {Austral Ecology},
-month = {dec},
-number = {4},
-pages = {363--378},
-title = {{How New Guinea rainforest flower resources vary in time and space: Implications for nectarivorous birds}},
-url = {http://doi.wiley.com/10.1111/j.1442-9993.1996.tb00623.x},
-volume = {21},
-year = {1996}
-}
-@article{Osazuwa-Peters2015a,
-abstract = {Selective logging, the targeted harvesting of timber trees in a single cutting cycle, is globally rising in extent and intensity. Short-term impacts of selective logging on tropical forests have been widely investigated, but long-term effects on temporal dynamics of forest structure and composition are largely unknown. Understanding these long-term dynamics will help determine whether tropical forests are resilient to selective logging and inform choices between competing demands of anthropogenic use versus conservation of tropical forests. Forest dynamics can be studied within the framework of succession theory, which predicts that temporal turnover rates should decline with time since disturbance. Here, we investigated the temporal dynamics of a tropical forest in Kibale National Park, Uganda over 45 years following selective logging. Weestimated turnover rates in stems, species composition, and functional traits (wood density and diameter at breast height), using observations from four censuses in 1989, 1999, 2006, and 2013, of stemsP10 cm diameter within 17 unlogged and 9 logged 200 ? 10m vegetation plots. We used null models to account for interdependencies among turnover rates in stems, species composition, and functional traits. We tested predictions that turnover rates should be higher and decrease with increasing time since the selective logging event in logged forest, but should be less temporally variable in unlogged forest. Overall, we found higher turnover rates in logged forest for all three attributes, but turnover rates did not decline through time in logged forest and was not less temporally variable in unlogged forest. These results indicate that successional models that assume recovery to predisturbance conditions are inadequate for predicting the effects of selective logging on the dynamics of the tropical forest in Kibale. Selective logging resulted in persistently higher turnover rates, which may compromise the carbon storage capacity of Kibale's forest. Selective logging effects may also interact with effects from other global trends, potentially causing major long-term shifts in the dynamics of tropical forests. Similar studies in tropical forests elsewhere will help determine the generality of these conclusions. Ultimately, the view that selective logging is a benign approach to the management of tropical forests should be reconsidered in the light of studies of the effects of this practice on long-term forest dynamics.},
-author = {Osazuwa-Peters, Oyomoare L. and Jim{\'{e}}nez, Iv{\'{a}}n and Oberle, Brad and Chapman, Colin A. and Zanne, Amy E.},
-doi = {10.1016/j.foreco.2015.08.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Osazuwa-Peters, Chapman, Zanne - 2015 - Selective logging does the imprint remain on tree structure and composition after 45 years.pdf:pdf},
-journal = {Forest Ecology and Management},
-pages = {10--21},
-title = {{Selective logging: Do rates of forest turnover in stems, species composition and functional traits decrease with time since disturbance? – A 45year perspective}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0378112715004181},
-volume = {357},
-year = {2015}
-}
-@article{Arbia2017,
-abstract = {Effects of missing data and locational errors on spatial concentration measures based on Ripley's K-function. Spatial Economic Analysis. Measures based on Ripley's K-function are the preferred tools to test the concentration of individual agents in an economic space. In many empirical cases, however, the datasets contain different inaccuracies due to missing data or uncertainty about the location of the agents. Little is known thus far about the effects of these inaccuracies on the K-function. This paper sheds light on the problem through a theoretical analysis supported by Monte Carlo experiments. The results show that patterns of clustering or inhibition may be observed not as genuine phenomena but only as the effect of data imperfections.},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego and Dickson, Maria Michela},
-doi = {10.1080/17421772.2017.1297479},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2017 - Effects of missing data and locational errors on spatial concentration measures based on Ripley's K -function.pdf:pdf},
-journal = {Spatial Economic Analysis},
-title = {{Effects of missing data and locational errors on spatial concentration measures based on Ripley's K -function}},
-url = {https://www.tandfonline.com/doi/full/10.1080/17421772.2017.1297479},
-volume = {in press},
-year = {2017}
-}
-@article{Kiskowski2009,
-abstract = {Ripley's K-, H-, and L-functions are used increasingly to identify clustering of proteins in membrane microdomains. In this approach, aggregation (or clustering) is identified if the average number of proteins within a distance r of another protein is statistically greater than that expected for a random distribution. However, it is not entirely clear how the function may be used to quantitatively determine the size of domains in which clustering occurs. Here, we evaluate the extent to which the domain radius can be determined by different interpretations of Ripley's K-statistic in a theoretical, idealized context. We also evaluate the measures for noisy experimental data and use Monte Carlo simulations to separate the effects of different types of experimental noise. We find that the radius of maximal aggregation approximates the domain radius, while identifying the domain boundary with the minimum of the derivative of H(r) is highly accurate in idealized conditions. The accuracy of both measures is impacted by the noise present in experimental data; for example, here, the presence of a large fraction of particles distributed as monomers and interdomain interactions. These findings help to delineate the limitations and potential of Ripley's K in real-life scenarios.},
-author = {Kiskowski, Maria A. and Hancock, John F. and Kenworthy, Anne K.},
-doi = {10.1016/j.bpj.2009.05.039},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kiskowski, Hancock, Kenworthy - 2009 - On the Use of Ripley's K-Function and Its Derivatives to Analyze Domain Size.pdf:pdf},
-journal = {Biophysical journal},
-number = {4},
-pages = {1095--1103},
-title = {{On the Use of Ripley's K-Function and Its Derivatives to Analyze Domain Size}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349509010480},
-volume = {97},
-year = {2009}
-}
-@article{Frontier1976,
-abstract = {The decrease of successive eigenvalues in some principal component analysis of 20 variates and 44 individuals, is compared with that of the 'broken stick' model, where a fixed length is broken at random into a number of segments. In the real analysis, the two first eigenvalues stay distinctly above the model values, indicating the occurrence of factors acting on the variables. Residual variance seems partitioned between other axes, according to a model which approaches the broken stick. The adjustment is not perfect, since an unknown part of the random variance also contributes to the first eigenvalues. The model, however, allows an empirical determination of the number of significant vectors. ?? 1976.},
-author = {Frontier, Serge},
-doi = {10.1016/0022-0981(76)90076-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Frontier - 1976 - {\'{E}}tude de la d{\'{e}}croissance des valeurs propres dans une analyse en composantes principales Comparaison avec le modd{\`{e}}le d.pdf:pdf},
-journal = {Journal of Experimental Marine Biology and Ecology},
-number = {1},
-pages = {67--75},
-title = {{{\'{E}}tude de la d{\'{e}}croissance des valeurs propres dans une analyse en composantes principales: Comparaison avec le modd{\`{e}}le du b{\^{a}}ton bris{\'{e}}}},
-volume = {25},
-year = {1976}
-}
-@article{Heinrich1991,
-abstract = {This paper suggests several tests for checking the nullhypothesis that a point pattern observed in a (large) rectangular sampling window D{\^{a}}{\v{S}}‚Rd belongs to a realization of a stationary Poisson Process based on test statistics measuring the distance between the empirical and the true second moment function {\^{A}} volume of the unit sphere im R d. We consider the case of known intensity and the case of estimated intensity separately. On the basis of weak convergence of the corresponding diviation processes on [0,R] (as D becomes large) to Gaussian Processes various analogues to the classical goodness-of-fit tests X 2 Kolmogorov-SMIRNOV, CRAMER-VON MISES test) are developed and discussed. Tabulated values of the test statistics based on simulated data compared with the quantiles of their limit distributions illustrate the applicability of the proposed tests},
-author = {Heinrich, L.},
-doi = {10.1080/02331889108802308},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Heinrich - 1991 - Goodness-of-fit tests for the second moment function of a stationary multidimensional poisson process.pdf:pdf},
-journal = {Statistics: A Journal of Theoretical and Applied Statistics},
-number = {2},
-pages = {245--268},
-title = {{Goodness-of-fit tests for the second moment function of a stationary multidimensional poisson process}},
-url = {http://www.informaworld.com/10.1080/02331889108802308},
-volume = {22},
-year = {1991}
-}
-@article{Darwin1859,
-abstract = {... he published his conviction that the same forms have not been perpetuated since the origin of all ... He was cautious in drawing conclusions, and did not believe that existing species are now ... In this paper he distinctly recognises the principle of natural selection , and this is the first ... $\backslash$n},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Darwin, Charles},
-doi = {10.1126/science.146.3640.51-b},
-eprint = {arXiv:1011.1669v3},
-isbn = {145381468X},
-issn = {0036-8075},
-journal = {London: Murray},
-pages = {247},
-pmid = {20439281},
-title = {{On the origins of species by means of natural selection}},
-url = {http://sciencestudies.pbworks.com/f/OoS.pdf},
-year = {1859}
-}
-@article{Horvitz1952,
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Horvitz, D. G. and Thompson, D. J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Horvitz, Thompson - 1952 - A generalization of sampling without replacement from a finite universe.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {260},
-pages = {663--685},
-title = {{A generalization of sampling without replacement from a finite universe}},
-volume = {47},
-year = {1952}
-}
-@article{Henderson1997,
-abstract = {Using panel data for five capital goods industries, this paper estimates dynamic externalities. In contrast to previous studies, panel data allow separation of externalities from fixed effects and identification of a lag structure. I find strong evidence of Marshall–Arrow–Romer (MAR) (own industry, or localization) externalities. For Jacobs (urbanization) externalities effects are smaller. In terms of lag structure, for MAR externalities the biggest effects are typically from several years ago, but die out after six years. For urbanization phenomena, effects persist to the end of the time horizon of the data–eight or nine years back.},
-author = {Henderson, Vernon},
-doi = {10.1006/juec.1997.2036},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Henderson - 1997 - Externalities and Industrial Development.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {3},
-pages = {449--470},
-title = {{Externalities and Industrial Development}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119097920362},
-volume = {42},
-year = {1997}
-}
-@article{Usinowicz2017,
-author = {Usinowicz, Jacob and Chang-Yang, Chia-Hao and Chen, Yu-Yun and Clark, James S. and Fletcher, Christine and Garwood, Nancy C. and Hao, Zhanqing and Johnstone, Jill and Lin, Yiching and Metz, Margaret R. and Masaki, Takashi and Nakashizuka, Tohru and Sun, I-Fang and Valencia, Renato and Wang, Yunyun and Zimmerman, Jess K. and Ives, Anthony R. and Wright, S. Joseph},
-doi = {10.1038/nature24038},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Usinowicz et al. - 2017 - Temporal coexistence mechanisms contribute to the latitudinal gradient in forest diversity.pdf:pdf},
-issn = {0028-0836},
-journal = {Nature},
-pmid = {28953870},
-publisher = {Nature Publishing Group},
-title = {{Temporal coexistence mechanisms contribute to the latitudinal gradient in forest diversity}},
-url = {http://www.nature.com/doifinder/10.1038/nature24038},
-year = {2017}
-}
-@article{Williamson2001,
-abstract = {Aim To attack a widespread myth. Location World-wide. Methods Simple mathematical logical and empirical examples. Results As both species and area are finite and non-negative, the species–area relationship is limited at both ends. The log species–log area relationship is normally effectively linear on scales from about 1 ha to 107 km2. There are no asymptotes. At the intercontinental scale it may get steeper; at small scales it may in different cases get steeper or shallower or maintain its slope. Main conclusion The species–area relationship does not have an asymptote.},
-author = {Williamson, Mark and Gaston, Kevin J. and Lonsdale, W. M.},
-doi = {10.1046/j.1365-2699.2001.00603.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Williamson, Gaston, Lonsdale - 2001 - The species–area relationship does not have an asymptote!.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {7},
-pages = {827--830},
-title = {{The species–area relationship does not have an asymptote!}},
-url = {http://dx.doi.org/10.1046/j.1365-2699.2001.00603.x},
-volume = {28},
-year = {2001}
-}
-@unpublished{Mori2014,
-abstract = {The standard approaches to studying industrial agglomeration have been in terms of summary measures of the “degree of agglomeration” within each industry. But such measures often fail to distinguish between industries that exhibit substantially different spatial scales of agglomeration. In a previous paper, Mori and Smith [45] proposed a new pair of quantitative measures for distinguishing both the scale and degree of industrial agglomeration based on an explicit method for detecting spatial clusters. The first, designated as the global extent (GE) of industrial clusters, measures the spatial spread of these clusters (within a given country) in terms of the areal size of their essential containment, defined to be the (convex-solid) region containing the most significant subset of these clusters. The second, designated as the local density (LD) of industrial clusters, measures the spatial extent of individual clusters within their essential containment in terms of the areal share of that containment occupied by clusters. The central purpose of the present paper is to apply these two measures to the manufacturing industries in Japan, and to demonstrate how they can be used in combination to distinguish both the relative scale and degree of agglomeration exhibited by cluster patterns for each industry. In addition, the information provided by this pair of measures (GE, LD) is systematically compared to that of the most prominent summary measures currently in use. Finally, it is shown that these measures also sup- port certain predictions of new economic geography models in the sense that shipping distances for establishments in each industry tend to be negatively (positively) correlated with the GE (LD) measures of agglomeration in these industries.},
-address = {Kyoto},
-author = {Mori, Tomoya and Smith, Tony E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mori, Smith - 2014 - On the Spatial Scale of Industrial Agglomerations.pdf:pdf},
-institution = {Kyoto University},
-series = {Kier Discussion Paper Series},
-title = {{On the Spatial Scale of Industrial Agglomerations}},
-year = {2014}
-}
-@article{Ricotta2014a,
-abstract = {Due to its nonlinearity with respect to species addition, some applications of the Rao quadratic diversity are mean- ingful only if they are first transformed into their equivalent number of species, which is the theoretical species richness of a maximally distinct and perfectly even community with the same diversity as the original community. In this paper, relaxing the requirement of maximal distinction among species, we generalize the notion of the equivalent number of species for the Rao diversity to partially distinct species. The biological meaning of this proposal is illustrated with one dedicated case study in sand dune communities in Italy. According to our results, the proposed approach proved appropriate for comparing the functional diversity of different plant communities with varying levels of environmental constraints.},
-author = {Ricotta, Carlo and Acosta, Alicia T.R.},
-doi = {10.1556/ComEc.15.2014.2.9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Acosta - 2014 - On the functional diversity of partially distinct species some theory and a practical example.pdf:pdf},
-journal = {Community Ecology},
-number = {2},
-pages = {205--211},
-title = {{On the functional diversity of partially distinct species: some theory and a practical example}},
-url = {http://www.akademiai.com/openurl.asp?genre=article{\&}id=doi:10.1556/ComEc.15.2014.2.9},
-volume = {15},
-year = {2014}
-}
-@article{Okuda1997a,
-abstract = {Three analyses of species diversity in a lowland dipterocarp forest were conducted to examine whether the nature of forest community dynamics are determined by density-dependent recruitment and mortality of saplings with a data set obtained in a 50 ha plot in Pasoh Forest Reserve. The first analysis examined whether sapling density varied as a function of distance from the nearest conspecific adult. The second analysis assessed the relationship between the spatial distribution patterns of saplings and adult trees. A third analysis examined sapling recruitment and mortality based on data from 2 censuses, taken in 1985 and 1990. Four hundred forty-four species (each with more than 100 individuals) out of the total of 814 species recorded in the plot, were chosen for the analyses. Of these selected species, 56 species showed significant reduction in sapling densities close to the conspecific adults. Within this group, 11 species were in the emergent layer (29.0{\%} of the total species in this layer), 17 were in the canopy layer (10.5{\%}), 18 were in the understory layer (11.3{\%}), and 10 were in treelet and shrub layer (11.8{\%}). In contrast, the sapling densities of 53 species decreased with increasing distance from conspecific adults; 2 of these species were in the emergent layer (5.2{\%} of the total species in this layer), 14 were in the canopy layer (8.6{\%}), 21 were in the understory layer (13.2{\%}), and 16 were in the treelet and shrub layer (18.8{\%}). The saplings of 35 of the 444 total selected species were clumped, while adults were regularly or randomly distributed. Of the remaining species, in 183 species (41.2{\%}), the distributions of both adults and saplings were clumped. Thus, these 2 analyses do not support the prediction that most of the species of lowland tropical forests fail to produce new adults in their vicinity and as a result of this, adult trees are more regularly distributed than their conspecific juveniles (Janzen 1970). In the third analysis, the recruitment of saplings of species in the emergent and canopy layers increased significantly and in proportion with mortality, suggesting that the dominant species suffer higher mortality than do less common species. This trend is not so apparent in the understory, and the treelet and shrub layers. The results imply that a dynamic equilibrium process, which prevents competitive exclusion and maintains space for minor species, may be active among the species in the upper layers (particularly the emergent layer); however, such a dynamic equilibrium condition is not due exclusively to the reduced recruitment of saplings near conspecific adults, and the dynamic equilibrium condition is not prevalent among the lower story species.},
-author = {Okuda, Toshinori and Kachi, Naoki and Yap, Son Kheong and Manokaran, N.},
-doi = {10.1023/A:1009727109920},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Okuda et al. - 1997 - Tree distribution pattern and fate of juveniles in a lowland tropical rain forest - Implications for regeneration.pdf:pdf},
-journal = {Plant Ecology},
-number = {2},
-pages = {155--171},
-title = {{Tree distribution pattern and fate of juveniles in a lowland tropical rain forest - Implications for regeneration and maintenance of species diversity}},
-volume = {131},
-year = {1997}
-}
-@article{Martens1997,
-abstract = {Semi-arid woodlands are two-phase mosaics of canopy and inter- canopy patches. It was hypothesized that both above-ground competition (within canopy patches), and below-ground competition (between canopy patches), would be important structuring processes in these communities. The spatial pattern of trees in a Pinus edulis-Juniperus monosperma woodland in New Mexico was investigated using Ripley's K-function. Strong aggregation of trees was found at scales of 2 to 4 m, which indicates the scale of canopy patches. Canopy patches were composed of individuals of both species. Crown centres of both species were always less aggregated than stem centres at scales less than canopy patch size, indicating morphological plasticity of competing crowns. In the smallest size classes of both species, aggregation was most intense, and occurred over a larger range of scales; aggregation decreased with increasing size as is consistent with density-dependent mortality from intraspecific competition. Within canopy patches, younger trees were associated with older trees of the other species. At scales larger than canopy patches, younger trees showed repulsion from older conspecifics, indicating below-ground competition. Hence, intraspecific competition was stronger than interspecific competition, probably because the species differ in rooting depth. Woodland dynamics depend on the scale and composition of canopy patches, aggregated seed deposition and facilitation, above- and below-ground competition, and temporal changes in the spatial scale of interactions. This woodland is intermediate in a grassland-forest continuum (a gradient of increasing woody canopy cover) and hence the effects of both above- and below-ground competition were detected.},
-author = {Martens, Scott N. and Breshears, David D. and Meyer, Clifton W. and Barnes, Fairley J.},
-doi = {10.2307/3237370},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Martens et al. - 1997 - Scales of above-ground and below-ground competition in a semi-arid woodland detected from spatial pattern.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {655--664},
-title = {{Scales of above-ground and below-ground competition in a semi-arid woodland detected from spatial pattern}},
-url = {http://www.jstor.org/stable/3237370},
-volume = {8},
-year = {1997}
-}
-@article{Tovo2016,
-abstract = {The quantification of tropical tree biodiversity worldwide remains an open and challenging problem. More than two-fifths of the number of worldwide trees can be found either in tropical or in subtropical forests, but only ≈0.000067{\%} of species identities are known. We introduce an analytical framework that provides robust and accurate estimates of species richness and abundances in biodiversity-rich ecosystems, as confirmed by tests performed on both in silico–generated and real forests. Our analysis shows that the approach outperforms other methods. In particular, we find that upscaling methods based on the log-series species distribution systematically overestimate the number of species and abundances of the rare species. We finally apply our new framework on 15 empirical tropical forest plots and quantify the minimum percentage cover that should be sampled to achieve a given average confidence interval in the upscaled estimate of biodiversity. Our theoretical framework confirms that the forests studied are comprised of a large number of rare or hyper-rare species. This is a signature of critical-like behavior of species-rich ecosystems and can provide a buffer against extinction.},
-author = {Tovo, Anna and Suweis, Samir and Formentin, Marco and Favretti, Marco and Volkov, Igor and Banavar, Jayanth R. and Azaele, Sandro and Maritan, Amos},
-doi = {10.1126/sciadv.1701438},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tovo et al. - 2017 - Upscaling species richness and abundances in tropical forests(2).pdf:pdf},
-journal = {Science Advances},
-number = {10},
-pages = {e1701438},
-title = {{Upscaling species richness and abundances in tropical forests}},
-url = {http://advances.sciencemag.org/content/3/10/e1701438},
-volume = {2},
-year = {2017}
-}
-@article{Sobek2009,
-abstract = {Aim Plant and arthropod diversity are often related, but data on the role of mature tree diversity on canopy insect communities are fragmentary. We compare species richness of canopy beetles across a tree diversity gradient ranging from mono-dominant beech to mixed stands within a deciduous forest, and analyse community composition changes across space and time. Location Germany's largest exclusively deciduous forest, the Hainich National Park (Thuringia). Methods We used flight interception traps to assess the beetle fauna of various tree species, and applied additive partitioning to examine spatiotemporal patterns of diversity. Results Species richness of beetle communities increased across the tree diversity gradient from 99 to 181 species per forest stand. Intra- and interspecific spatial turnover among trees contributed more than temporal turnover among months to the total c-beetle diversity of the sampled stands. However, due to parallel increases in the number of habitat generalists and the number of species in each feeding guild (herbivores, predators and fungivores), no proportional changes in community composition could be observed. If only beech trees were analysed across the gradient, patterns were similar but temporal (monthly) species turnover was higher compared to spatial turnover among trees and not related to tree diversity. Main conclusions The changes in species richness and community composition across the gradient can be explained by habitat heterogeneity, which increased with the mix of tree species. We conclude that understanding temporal and spatial species turnover is the key to understanding biodiversity patterns. Mono- dominant beech stands are insufficient to conserve fully the regional species richness of the remaining semi-natural deciduous forest habitats in Central Europe, and analysing beech alone would have resulted in the misleading conclusion that temporal (monthly) turnover contributes more to beetle diversity than spatial turnover among different tree species or tree individuals.},
-author = {Sobek, Stephanie and Steffan-Dewenter, Ingolf and Scherber, Christoph and Tscharntke, Teja},
-doi = {10.1111/j.1472-4642.2009.00570.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sobek et al. - 2009 - Spatiotemporal changes of beetle communities across a tree diversity gradient.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {4},
-pages = {660--670},
-title = {{Spatiotemporal changes of beetle communities across a tree diversity gradient}},
-url = {http://doi.wiley.com/10.1111/j.1472-4642.2009.00570.x},
-volume = {15},
-year = {2009}
-}
-@book{Hodder1976,
-address = {London},
-author = {Hodder, I. and Orton, C.},
-isbn = {0 521 29738 9},
-pages = {1--270},
-publisher = {Cambridge University Press},
-title = {{Spatial Analysis in Archaeology}},
-year = {1976}
-}
-@misc{Franc2001,
-author = {Franc, Alain},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Franc - 2001 - Introduction aux processus stochastiques.pdf:pdf},
-keywords = {Franc (2001).pdf},
-mendeley-tags = {Franc (2001).pdf},
-pages = {44},
-title = {{Introduction aux processus stochastiques}},
-year = {2001}
-}
-@book{Stoyan1994,
-abstract = {In Part I the reader is introduced to the methods of measuring the fractal dimension of irregular geometric structures. Part II demonstrates important modern methods for the statistical analysis of random shapes. The statistical theory of point fields, with and without marks, is introduced in Part III. Each of the three sections concentrates on the mathematical ideas, rather than detailed proofs, and can be read independently.},
-address = {Chichester},
-author = {Stoyan, Dietrich and Stoyan, Helga},
-doi = {978-0-471-93757-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan, Stoyan - 1994 - Fractals, Random Shapes and Point Fields Methods of Geometrical Statistics.pdf:pdf},
-publisher = {John Wiley {\&} Sons},
-title = {{Fractals, Random Shapes and Point Fields: Methods of Geometrical Statistics}},
-url = {http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471937576.html},
-year = {1994}
-}
-@article{Tsallis1998,
-abstract = {The Gibbs–Jaynes path for introducing statistical mechanics is based on the adoption of a specific entropic form Sand of physically appropriate constraints. For instance, for the usual canonical ensemble, one adopts (i) Full-size image ({\textless}1 K), (ii) ∑ipi=1, and (iii) Full-size image ({\textless}1 K) ({\{}$\epsilon$i{\}}≡ eigenvalues of the Hamiltonian; U1≡ internal energy). Equilibrium consists in optimizing S1 with regard to {\{}pi{\}} in the presence of constraints (ii) and (iii). Within the recently introduced nonextensive statistics, (i) is generalized into Sq=k[1−∑ipiq]/[q−1] (q→1 reproduces S1), (ii) is maintained, and (iii) is generalized in a manner which might involve piq. In the present effort, we analyze the consequences of some special choices for (iii), and their formal and practical implications for the various physical systems that have been studied in the literature. To illustrate some mathematically relevant points, we calculate the specific heat respectively associated with a nondegenerate two-level system as well as with the classical and quantum harmonic oscillators.},
-author = {Tsallis, Constantino and Mendes, R. S. and Plastino, Angel R.},
-doi = {10.1016/S0378-4371(98)00437-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsallis, Mendes, Plastino - 1998 - The role of constraints within generalized nonextensive statistics.pdf:pdf},
-journal = {Physica A},
-number = {3},
-pages = {534--554},
-title = {{The role of constraints within generalized nonextensive statistics}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378437198004373},
-volume = {261},
-year = {1998}
-}
-@article{Rowlingson1993,
-abstract = {In recent years, Geographical Information Systems have provided researchers in many fields with facilities for mapping and analyzing spatially referenced data. Commercial systems have excellent facilities for database handling and a range of spatial operations. However, none can claim to be a rich environment for statistical analysis of spatial data. We have made some powerful enhancements to the S-Plus system to produce a tool for display and analysis of spatial point pattern data. In this paper we give a brief introduction to the S-Plus system and a detailed description of the S-Plus enhancements. We then present three worked examples: two from geomorphology and one from epidemiology.},
-author = {Rowlingson, Barry S. and Diggle, Peter J.},
-doi = {10.1016/0098-3004(93)90099-Q},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rowlingson, Diggle - 1993 - SPLANCS Spatial Point Pattern Analysis Code in S-Plus.pdf:pdf},
-journal = {Computers {\&} Geosciences},
-number = {5},
-pages = {627--655},
-title = {{SPLANCS: Spatial Point Pattern Analysis Code in S-Plus}},
-url = {http://www.sciencedirect.com/science/article/pii/009830049390099Q},
-volume = {19},
-year = {1993}
-}
-@article{Sinclair1985,
-author = {Sinclair, Dennis F.},
-doi = {10.2307/1940568},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sinclair - 1985 - On Tests of Spatial Randomness Using Mean Nearest Neighbor Distance.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {1084--1085},
-title = {{On Tests of Spatial Randomness Using Mean Nearest Neighbor Distance}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1940568/abstract},
-volume = {66},
-year = {1985}
-}
-@article{Gotzenberger2012,
-abstract = {Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co-occur randomly but are restricted in their co-occurrence by interspecific competition. This concept can be redefined in a more general framework where the co-occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta-analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co-occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta-analyses suggest that non-random co-occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non-random aspect of assembly in plant communities.},
-author = {G{\"{o}}tzenberger, Lars and de Bello, Francesco and Br{\aa}then, Kari Anne and Davison, John and Dubuis, Anne and Guisan, Antoine and Lep{\v{s}}, Jan and Lindborg, Regina and Moora, Mari and P{\"{a}}rtel, Meelis and Pellissier, Loic and Pottier, Julien and Vittoz, Pascal and Zobel, Kristjan and Zobel, Martin},
-doi = {10.1111/j.1469-185X.2011.00187.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/G{\"{o}}tzenberger et al. - 2012 - Ecological assembly rules in plant communities - approaches, patterns and prospects.pdf:pdf},
-journal = {Biological Reviews},
-number = {1},
-pages = {111--127},
-title = {{Ecological assembly rules in plant communities - approaches, patterns and prospects}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2011.00187.x/abstract},
-volume = {87},
-year = {2012}
-}
-@article{Sukumaran2017,
-abstract = {The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.},
-author = {Sukumaran, Jeet and Knowles, L. Lacey},
-doi = {10.1073/PNAS.1607921114},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sukumaran, Knowles - 2017 - Multispecies coalescent delimits structure, not species.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-title = {{Multispecies coalescent delimits structure, not species}},
-url = {http://www.pnas.org/content/early/2017/01/25/1607921114},
-volume = {in press},
-year = {2017}
-}
-@article{Violle2017,
-abstract = {Rarity has been a central topic for conservation and evolutionary biologists aiming to determine the species characteristics that cause extinction risk. More recently, beyond the rarity of species, the rarity of functions or functional traits, called functional rarity, has gained momentum in helping to understand the impact of biodiversity decline on ecosystem functioning.However, a conceptual framework for defining and quantifying functional rarity is still lacking. We introduce 12 different forms of functional rarity along gradients of species scarcity and trait distinctiveness. We then highlight the potential key role of functional rarity in the long-term and large-scale maintenance of ecosystem processes, as well as the necessary linkage between functional and evolutionary rarity.},
-author = {Violle, Cyrille and Thuiller, Wilfried and Mouquet, Nicolas and Munoz, Fran{\c{c}}ois and Kraft, Nathan J. B. and Cadotte, Marc W. and Livingstone, Stuart W. and Mouillot, David},
-doi = {10.1016/j.tree.2017.02.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Violle et al. - 2017 - Functional Rarity The Ecology of Outliers.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-title = {{Functional Rarity: The Ecology of Outliers}},
-url = {http://www.elsevier.com/artworkinstructions.},
-volume = {in press},
-year = {2017}
-}
-@article{Holyoak2006,
-abstract = {Neutral community models embody the idea that individuals are ecologically equivalent, having equal fitness over all environmental conditions, and describe how the spatial dynamics and speciation of such individuals can produce a wide range of patterns of distribution, diversity, and abundance. Neutral models have been controversial, provoking a rush of tests and comments. The debate has been spurred by the suggestion that we should test mechanisms. However, the mechanisms and the spatial scales of interest have never clearly been described, and consequently, the tests have often been only peripherally relevant. At least two mechanisms are present in spatially structured neutral models. Dispersal limitation causes clumping of a species, which increases the strength of intraspecific competition and reduces the strength of interspecific competition. This may prolong coexistence and enhance local and regional diversity. Speciation is present in some neutral models and gives a donor-controlled input of new species, many of which remain rare or are short lived, but which directly add to species diversity. Spatial scale is an important consideration in neutral models. Ecological equivalence and equal fitness have implicit spatial scales because dispersal limitation and its emergent effects operate at population levels, and populations and communities are defined at a chosen spatial scale in recent neutral models; equality is measured relative to a metacommunity, and this necessitates defining the spatial scale of that metacommunity. Furthermore, dispersal has its own scales. Thorough empirical tests of neutral models will require both tests of mechanisms and pattern-producing ability, and will involve coupling theoretical models and experiments. Key},
-author = {Holyoak, M. and Loreau, Michel},
-doi = {10.1890/0012-9658(2006)87[1370:REEWNC]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holyoak, Loreau - 2006 - Reconciling empirical ecology with neutral community models.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1370--1377},
-title = {{Reconciling empirical ecology with neutral community models}},
-url = {http://www.esajournals.org/doi/abs/10.1890/0012-9658(2006)87{\%}255B1370:REEWNC{\%}255D2.0.CO{\%}253B2},
-volume = {87},
-year = {2006}
-}
-@article{Lohbeck2014,
-abstract = {1. Deterministic theories predict that local communities assemble from a regional species pool based on niche differences, thus by plant functional adaptations. We tested whether functional traits can also explain patterns in species dominance among the suite of co-occurring species. 2. We predicted that along a gradient of secondary succession, the main driver of species dom- inance changes from environmental filtering in the relatively harsh (dry and hot) early succes- sional conditions, towards increased competitive interactions and limiting similarity in later successional conditions (when light is limited). 3. We used the Kurtosis (K) (a measure of peakedness) of the functional trait distribution of secondary forest communities in high-diversity tropical rain forest in Chiapas, Mexico. The forests ranged 1–25 years in age, and we used eight functional leaf traits related to a plants' carbon, water and heat balance. We calculated the functional trait distribution based on spe- cies dominance, where trait values were weighted by species' relative basal area, as well as based on species presence, all species counting once. ‘K-ratio' was subsequently computed by dividing kurtosis based on species dominance by kurtosis based on species presence. If the K-ratio is high, the dominant species are functionally similar and we interpreted this as environ- mentally driven functional convergence allowing species to become dominant. If the K-ratio is small, dominant species are a functionally dissimilar subset of the species present and we inter- preted this as competitively driven functional divergence allowing species to become dominant. 4. We found that in early succession, dominant species represent a functionally narrow subset of species with similar traits, and in late succession, dominant species increasingly represent a wide subset of the species present. This trend was found for traits that reflect photosynthetic performance and light capture, and indicates increased competition for light with succession. No trend was found for traits that indicate defence against herbivory, suggesting no succes- sional changes in herbivore pressure. 5. Synthesis. This is one of the first studies showing that drivers of species dominance change along a gradient of secondary succession. During the early successional time window we evalu- ated, the importance of environmental filtering as a driving force fades away rapidly, and the importance of niche partitioning for species dominance starts to emerge.},
-author = {Lohbeck, Madelon and Poorter, Lourens and Mart{\'{i}}nez-Ramos, Miguel and Rodriguez-Vel{\'{a}}zquez, Jorge and van Breugel, Michiel and Bongers, Frans},
-doi = {10.1111/1365-2435.12240},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lohbeck et al. - 2014 - Changing drivers of species dominance during tropical forest succession.pdf:pdf},
-journal = {Functional Ecology},
-number = {4},
-pages = {1052--1058},
-title = {{Changing drivers of species dominance during tropical forest succession}},
-url = {http://doi.wiley.com/10.1111/1365-2435.12240},
-volume = {28},
-year = {2014}
-}
-@article{Hargreaves2008,
-abstract = {A more or less random selection of the international journal literature on the subject of phytosociology in Brazil with publication dates from 1998 to 2007 is reviewed. The 90 papers are reviewed on the basis of three fundamental themes. First by their coverage of the various plant physiognomies that can be found in Brazil, and indeed throughout much of the Neotropics: phytoplankton, fungi, lichen, ferns, aroids, epiphytic orchids and bromeliads, Velloziaceae, palms, grasses, bamboo, succulents, stranglers, trees, shrubs and lianas. Then as representative of the Brazilian biomes: Amazon Biome, Cerrado Biome, Caatinga Biome, Pantanal Biome, Atlantic Forest Biome, and Coastal and Island Biome, there being none for the Pampa Biome. Finally, from a more critical viewpoint they are examined for their coverage of the environmental factors that help determine composition and structure of plant communities. The phytosociological methods for the predominantly woody plants and related multivariate data analysis are also briefly described. Many uses have been made of the results of phytosociological surveys, highlighting Brazil as a macrocosm of plant community ecology and vegetation science.},
-author = {Hargreaves, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hargreaves - 2008 - Phytosociology in Brazil.pdf:pdf},
-journal = {The Americas Journal of Plant Science and Biotechnology},
-number = {2},
-pages = {12--20},
-title = {{Phytosociology in Brazil}},
-url = {http://www.globalsciencebooks.info/Online/GSBOnline/OnlineAmJPSB{\_}2{\_}1{\_}2.html},
-volume = {2},
-year = {2008}
-}
-@unpublished{Dumais1997,
-abstract = {has declined only slightly in the last twenty years. At the same time, new plant births, plant expansions, contractions and closures have shifted large quantities of employment across plants, firms, and locations. This paper uses data from the Census Bureau's Longitudinal Research Database to examine how relatively stable levels of geographic concentration emerge from this dynamic process. While industries' agglomeration levels tend to remain fairly constant, we find that there is greater variation in the locations of these agglomerations. We then decompose aggregate concentration changes into portions attributable to plant births, expansions, contractions, and closures, and find that the location choices of new firms and differences in growth rates have played the most significant role in reducing levels of geographic concentration, while plant closures have tended to reinforce agglomeration. Finally, we look at coagglomeration patterns to test three of Marshall's theories of industry agglomeration: (1) agglomeration saves transport costs by proximity to input suppliers or final consumers, (2) agglomeration allows for labor market pooling, and (3) agglomeration facilitates intellectual spillovers. While there is some truth behind all three theories, we find that industrial location is far more driven by labor mix than by any of the other explanatory variables.},
-address = {Cambridge},
-author = {Dumais, Guy and Ellison, Glenn and Glaeser, Edward L},
-booktitle = {NBER Working Paper},
-doi = {10.3386/w6270},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dumais, Ellison, Glaeser - 1997 - Geographic Concentration as a Dynamic Process.pdf:pdf},
-pages = {47},
-title = {{Geographic Concentration as a Dynamic Process}},
-url = {http://www.nber.org/papers/w6270},
-volume = {6270},
-year = {1997}
-}
-@article{Borda-de-Agua2002,
-abstract = {Although fractals have been applied in ecology for some time, multifractals have, in contrast, received little attention. In this article, we apply multifractals to the species-area relationship and species abundance distributions. We highlight two results: first, species abundance distributions collected at different spatial scales may collapse into a single curve after appropriate renormalization, and second, the power-law form of the species-area relationship and the Shannon, Simpson, and Berger-Parker diversity indices belong to a family of equations relating the species number, species abundance, and area through the moments of the species abundance-probability density function. Explicit formulas for these diversity indices, as a function of area, are derived. Methods to obtain the multifractal spectra from a data set are discussed, and an example is shown with data on tree and shrub species collected in a 50-ha plot on Barro Colorado Island, Panama. Finally, we discuss the implications of the multifractal formalism to the relationship between species range and abundance and the relation between the shape of the species abundance distribution and area.},
-author = {Borda-de-{\'{A}}gua, Lu{\'{i}}s and Hubbell, Stephen P. and McAllister, Murdoch},
-doi = {10.1086/324787},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borda-de-{\'{A}}gua, Hubbell, McAllister - 2002 - Species-area curves, diversity indices, and species abundance distributions a multifractal a.pdf:pdf},
-journal = {The American naturalist},
-number = {2},
-pages = {138--155},
-title = {{Species-area curves, diversity indices, and species abundance distributions: a multifractal analysis.}},
-volume = {159},
-year = {2002}
-}
-@article{Brix2001,
-abstract = {We propose an extension of the classical complete spatial randomness tests to non- stationary Poisson spatial processes. The method consists of first performing the classical tests locally and then grouping the local results into a global test. The global test is a test for nonstationary Poisson process assumption, whereas the local tests can be used in an exploratory way to decide whether the observed process is locally regular or clustered or if we do not reject the inhomogeneous Poisson assumption. Under a Cox assumption, an optimal partition of the sampling window can be derived. Finally, we present some examples from forestry and weed sciences. Some},
-author = {Brix, Anders and Senoussi, Rachid and Couteron, Pierre and Chadoeuf, Jo{\"{e}}l},
-doi = {10.1093/biomet/88.2.487},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brix et al. - 2001 - Assessing goodness of fit of spatially inhomogeneous Poisson processes.pdf:pdf},
-journal = {Biometrika},
-number = {2},
-pages = {487--497},
-title = {{Assessing goodness of fit of spatially inhomogeneous Poisson processes}},
-url = {https://academic.oup.com/biomet/article-lookup/doi/10.1093/biomet/88.2.487},
-volume = {88},
-year = {2001}
-}
-@article{Norris1998,
-abstract = {The proper management of an ecological population is greatly aided by solid information about its species' abundances. For the general heterogeneous Poisson species abundance setting, we develop the non-parametric mle for the entire probability model, namely for the total number N of species and the generating distribution F for the expected values of the species' abundances. Solid estimation of the entire probability model allows us to develop generator-based measures of ecological diversity and evenness which have inferences over similar regions. Also, our methods produce a solid goodness-of-fit test for our model as well as a likelihood ratio test to examine if there is heterogeneity in the expected values of the species' abundances. These estimates and tests are examined, in detail, in the paper. In particular, we apply our methods to important data from the National Breeding Bird Survey and discuss how our methods can also be easily applied to sweep net sampling data. To further examine our methods, we provide simulations for several illustrative situations.},
-author = {Norris, J. L. and Pollock, K. H.},
-doi = {10.1023/A:1009659922745},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Norris, Pollock - 1998 - Non-parametric MLE for Poisson species abundance models allowing for heterogeneity between species.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {4},
-pages = {391--402},
-title = {{Non-parametric MLE for Poisson species abundance models allowing for heterogeneity between species}},
-url = {https://link.springer.com/article/10.1023/A:1009659922745},
-volume = {5},
-year = {1998}
-}
-@article{QIAN2011,
-abstract = {The latitudinal diversity gradient (LDG) has been known for over a century, but its origin remains poorly understood. Because both latitude and species richness are broadly related to temperature, environmental temperature has been proposed as a driver of the LDG. Recently, Wang et al. (2009, Proceedings of the National Academy of Sciences USA, 106,13388–13392) used datasets compiled from tree distributions in eastern Asia and North America to compare the species richness−temperature relationship between the two regions at several spatial scales and framed their analyses in the context of the metabolic theory of ecology. Here, we show that their datasets lack comparability between eastern Asia and North America and that some aspects of their analyses probably biased their results, casting doubt on some of their conclusions.},
-author = {Qian, Hong and Ricklefs, Robert E.},
-doi = {10.1111/j.1466-8238.2010.00590.x},
-issn = {1466822X},
-journal = {Global Ecology and Biogeography},
-month = {mar},
-number = {2},
-pages = {362--365},
-title = {{Latitude, tree species diversity and the metabolic theory of ecology}},
-url = {http://doi.wiley.com/10.1111/j.1466-8238.2010.00590.x},
-volume = {20},
-year = {2011}
-}
-@article{Hubbell1999,
-abstract = {Light gap disturbances have been postulated to play a major role in maintaining tree diversity in species-rich tropical forests. This hypothesis was tested in more than 1200 gaps in a tropical forest in Panama over a 13-year period. Gaps increased seedling establishment and sapling densities, but this effect was nonspecific and broad-spectrum, and species richness per stem was identical in gaps and in nongap control sites. Spatial and temporal variation in the gap disturbance regime did not explain variation in species richness. The species composition of gaps was unpredictable even for pioneer tree species. Strong recruitment limitation appears to decouple the gap disturbance regime from control of tree diversity in this tropical forest.},
-author = {Hubbell, Stephen P. and Foster, Robin B. and O'Brien, S.T. and Harms, Kyle E. and Condit, Richard and Wechsler, B. and Wright, S. Joseph and {Loo de Lao}, S.},
-doi = {10.1126/science.283.5401.554},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hubbell - 1999 - Light-Gap Disturbances, Recruitment Limitation, and Tree Diversity in a Neotropical Forest.pdf:pdf},
-journal = {Science},
-number = {5401},
-pages = {554--557},
-title = {{Light-Gap Disturbances, Recruitment Limitation, and Tree Diversity in a Neotropical Forest}},
-url = {http://www.sciencemag.org/content/283/5401/554.short},
-volume = {283},
-year = {1999}
-}
-@article{Arbuthnott1710,
-author = {Arbuthnott, John},
-doi = {10.1098/rstl.1710.0011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbuthnott - 1710 - An argument for divine providence, taken from the constant regularity observed in the births of both sexes.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London},
-pages = {186--190},
-title = {{An argument for divine providence, taken from the constant regularity observed in the births of both sexes}},
-url = {http://rstl.royalsocietypublishing.org/content/27/325-336/186},
-volume = {27},
-year = {1710}
-}
-@techreport{Conceicao2000a,
-address = {Austin, Texas},
-author = {Concei{\c{c}}{\~{a}}o, Pedro and Galbraith, James K and Bradford, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Concei{\c{c}}{\~{a}}o, Galbraith, Bradford - 2000 - The Theil Index in Sequences of Nested and Hierarchic Grouping Structures Implications for the M.pdf:pdf},
-pages = {43},
-publisher = {University of Texas},
-title = {{The Theil Index in Sequences of Nested and Hierarchic Grouping Structures: Implications for the Measurement of Inequality through Time with Data Aggregated at Different Levels of Industrial Classification}},
-url = {http://utip.gov.utexas.edu/web/workingpaper/utip15.pdf},
-year = {2000}
-}
-@article{Kohyama2006,
-abstract = {The effect of patch demography on the structure of forest tree communities was examined using a patch-age and tree-size structured model of forest dynamics. Changes in abundance of species of different types (four different maximum tree-size classes each in two or three shade-tolerance classes) were numerically modeled in response to changes in the duration of the gap-formation-free lag phase. Average patch mortality was identical in all simulations. Tolerant species were more abundant without a lag phase due to larger variation in patch longevity, while subtolerant or intolerant species were successful when patch longevity was fixed with a long duration of lag phase. Variation in patch-age distribution facilitated species coexistence. Increasing ‘advance regeneration', or surviving fraction at gap formation, brought about the exclusive dominance of the tolerant species. Results suggest that patch demography plays a significant role in the community organization of forest trees. In species-rich systems like tropical rain forests, longevity or canopy duration of large trees can differ among species, which brings about the variation in patch longevity, thus promoting further coexistence of species.},
-annote = {TY - JOUR},
-author = {Kohyama, Takashi},
-doi = {10.1007/s11284-006-0168-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kohyama - 2006 - The effect of patch demography on the community structure of forest trees.pdf:pdf},
-journal = {Ecological Research},
-number = {3},
-pages = {346--355},
-title = {{The effect of patch demography on the community structure of forest trees}},
-url = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}id=doi:10.1007/s11284-006-0168-8},
-volume = {21},
-year = {2006}
-}
-@article{Gotelli2006,
-abstract = {The neutral model posits that random variation in extinction and speciation events, coupled with limited dispersal, can account for many community properties, including the relative abundance distribution. There are important analogies between this model in ecology and a three-tiered hierarchy of models in evolution (Hardy Weinburg, drift, drift and selection). Because it invokes random processes and is used in statistical tests of empirical data, the neutral model can be interpreted as a specialized form of a null model. However, the application and interpretation of neutral models differs from that of standard null models in three important ways: 1) whereas most null models incorporate species-level constraints that are often associated with niche differences, the neutral model assumes that all species are functionally equivalent. 2) Null models are usually fit with constraints that are measured directly from the data set itself. In contrast, the neutral model requires parameters for speciation, extinction, and migration rates that are almost never measured directly, so their values must be guessed at or fitted. 3) Most important, null models are viewed as simple statistical descriptors: unspecified ''random'' forces generate variation in a simple model that excludes particular biological mechanisms (usually species interactions). Although the neutral model was originally framed as a null model, recent proponents of the neutral model have begun to treat it as a literal process-based description of community assembly. These differences lie at the heart of much of the recent controversy over the neutral model. If the neutral model is truly a process-based model, then its assumptions should be directly tested, and its predictions should be compared to those of an appropriate null model. Such tests are rarely informative, and most empirical data sets can be fit more parsimoniously to a simple log-normal distribution. Because unknown parameters in the neutral model must usually be guessed at or fit in ad-hoc ways, classical frequentist tests are compromised, and may be biased towards finding a good fit with the model. There has been little analysis of the potential for type I and type II errors in statistical tests of the neutral model. The neutral model has recently been proposed as a specific form of more general null models in biogeography (the mid-domain effect) and community ecology (species co-occurrence). In both cases, the neutral model is qualitatively, but not quantitatively, similar to the predictions of classic null models. However, because the important parameters in the neutral model can rarely be measured directly, it may be of limited value as a null hypothesis for empirical tests. Future progress may come from moving beyond dichotomous tests of neutral versus null models. Instead, the neutral model might be viewed as a mechanism that contributes to pattern along with other processes. Alternatively, the fit of data to the neutral model can be compared to the fit to other process-based models that are not based on neutrality assumptions. Finally, the neutral model can also be tested directly if its parameters can be estimated independently of the test data. However, these approaches may require more data than are often available. For these reasons, simple null model tests will continue to be important in the evaluation of the neutral model. The neutral model (Bell 2000, Hubbell 2001) has generated great interest and controversy among ecolo-gists. Some of these debates echo earlier controversies in the 1980s over null model analysis (Gotelli and Graves 1996). Indeed, Enquist et al. (2002) have claimed that the neutral model is nothing more or less than a null model. Yet there remains considerable confusion about whether the neutral theory is only a null model, can function as a null model, or is different from traditional null models. In this commentary, we review the similarities and differences between null and neutral models, and point out that a failure to clearly distinguish between them has been responsible for some of the controversy surround-ing neutral models.},
-author = {Gotelli, Nicholas J. and McGill, Brian J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gotelli, McGill - 2006 - Null versus neutral models what's the difference.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {793--800},
-title = {{Null versus neutral models: what's the difference?}},
-volume = {29},
-year = {2006}
-}
-@article{Wiegand2004,
-abstract = {A large number of methods for the analysis of point pattern data have been developed in a wide range of scientific fields. First-order statistics describe large-scale variation in the intensity of points in a study region, whereas second-order characteristics are summary statistics of all point-to-point distances in a mapped area and offer the potential for detecting both different types and scales of patterns. Second-order analysis based on Ripley's K-function is increasingly used in ecology to characterize spatial patterns and to develop hypothesis on underlying processes; however, the full range of available methods has seldomly been applied by ecologists. The aim of this paper is to provide guidance to ecologists with limited experience in second-order analysis to help in the choice of appropriate methods and to point to practical difficulties and pitfalls. We review (1) methods for analytical and numerical implementation of two complementary second-order statistics, Ripley's K and the O-ring statistic, (2) methods for edge correction, (3) methods to account for first-order effects (i.e. heterogeneity) of univariate patterns, and (4) a variety of useful standard and non-standard null models for univariate and bivariate patterns. For illustrative purpose, we analyze examples that deal with non-homogeneous univariate point patterns. We demonstrate that large-scale heterogeneity of a point-pattern biases Ripley's K-function at smaller scales. This bias is difficult to detect without explicitly testing for homogeneity, but we show that it can be removed when applying methods that account for first-order effects. We synthesize our review in a number of step-by-step recommendations that guide the reader through the selection of appropriate methods and we provide a software program that implements most of the methods reviewed and developed here.},
-annote = {ISI Document Delivery No.: 772NV},
-author = {Wiegand, Thorsten and Moloney, Kirk A.},
-journal = {Oikos},
-number = {2},
-pages = {209--229},
-title = {{Rings, circles, and null-models for point pattern analysis in ecology}},
-url = {http://www.blackwellpublishing.com},
-volume = {104},
-year = {2004}
-}
-@phdthesis{Daniel2001a,
-address = {Paris},
-author = {Daniel, Karine},
-publisher = {Universit{\'{e}} de Paris I},
-title = {{Politique agricole et localisation des activit{\'{e}}s dans l'Union europ{\'{e}}enne - Une analyse en {\'{e}}conomie g{\'{e}}ographique}},
-year = {2001}
-}
-@incollection{Lewontin1972,
-abstract = {It has always been obvious that organisms vary, even to those pre-Darwinian idealists who saw most individual variation as distorted shadows of an ideal. It has been equally apparent, even to those post-Darwinians for whom variation between individuals is the central fact of evolutionary dynamics, that variation is nodal, that individuals fall in clusters in the space of phenotypic description, and that those clusters, which we call demes, or races, or species, are the outcome of an evolutionary process acting on the individual variation. What has changed during the evolution of scientific thought, and is still changing, is our perception of the relative importance and extent of intragroup as opposed to intergroup variation. These changes have been in part a reflection of the uncovering of new biological facts, but only in part. They have also reflected general sociopolitical biases derived from human social experience and carried over into “scientific” realms. I have discussed elsewhere (Lewontin, 1968) long-term trends in evolutionary doctrine as a reflection of long-term changes in socioeconomic relations, but even in the present era of Darwinism there is considerable diversity of opinion about the amount or importance of intragroup variation as opposed to the variation between races and species. Muller, for example (1950), maintained that for sexually reproducing species, man in particular, there was very little genetic variation within populations and that most men were homozygous for wild-type genes at virtually all their loci.},
-author = {Lewontin, R.C.},
-booktitle = {Evolutionary Biology},
-doi = {10.1007/978-1-4684-9063-3_14},
-editor = {Dobzhansky, Theodosius and Hecht, Max K. and Steere, William C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lewontin - 1972 - The apportionment of human diversity(2).pdf:pdf},
-pages = {381--398},
-publisher = {Springer US},
-title = {{The apportionment of human diversity}},
-url = {http://link.springer.com/chapter/10.1007/978-1-4684-9063-3{\_}14},
-volume = {6},
-year = {1972}
-}
-@article{Holmes1999,
-abstract = {Theory suggests that vertical disintegration should be greater in areas where industries localize. This paper provides some evidence that this implication is true for the U.S. manufacturing sector. Purchased inputs as a percent of the value of output is used as a measure of vertical disintegration. To measure the localization of industry, for each manufacturing plant the amount of employment in neighboring plants in the same industry is determined.},
-author = {Holmes, Thomas J.},
-doi = {10.1162/003465399558102},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holmes - 1999 - Localization of Industry and Vertical Disintegration.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {2},
-pages = {314--325},
-title = {{Localization of Industry and Vertical Disintegration}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/003465399558102},
-volume = {81},
-year = {1999}
-}
-@article{Velazquez2015,
-abstract = {Aim: Community assembly theory predicts that niche differentiation promotes the spatial clustering of functionally dissimilar species, whereas habitat filtering has the converse effect.We used these predictions to assess the relative effects of habitat filtering and niche differentiation on recruit community assembly over spatial (5- and 30-mneighbourhoods) and temporal (20-yr) scales in the Forest Dynamics Plot at Barro Colorado Island. Location: Barro Colorado Island, Panama. Methods:We integrated data on the spatial patterns of =1 cmDBH(diameter at 1.3 mabove ground) recruitswith data on seven functional traits for 64 species. First, we quantified the interspecific association patterns of all species pairs i and j using the K-function Kij(r) and the nearest-neighbour distribution function Dij(r). Second, for those pairs with significant spatial associations, we calculated an index of interspecific spatial association using the results of these two sum- mary statistics. Finally, we examined the relationship between interspecific spatial association and trait similarity using simple and partialMantel tests. Results: In all censuses, almost one-half of species pairs had no spatial associa- tions, but for pairs that were significantly spatially associated, positive relation- ships between trait similarity and spatial association occurred in 5-m and 30-m neighbourhoods, whereas significant negative relationships only appeared in 5-m neighbourhoods. This suggests that habitat filtering was more important than niche differentiation in assembling recruit communities at 5- and 30-m scales. Habitat filtering mainly acted upon traits related to topographic habitat preferences and dispersal mode, whereas spatial association was inversely related to similarity in terms of wood specific gravity and shade tolerance. Conclusions: Our findings suggest that both stochastic and deterministic pro- cesses operate in species-rich ecological communities, but the role of habitat fil- tering and niche differentiation as determinants of community assembly vary over spatial and temporal scales. Species co-occurrencewas driven by habitat fil- tering at small and large scales, but also by a combination of niche differentiation and weaker-competitor exclusion effects at small scales. Temporal variations in the importance of habitat filtering and niche differentiation could be related to the occurrence of disturbances such as tree falls. Our results emphasize the role of trait-based processes in plant community assembly.},
-author = {Vel{\'{a}}zquez, Eduardo and Paine, C. E. Timothy and May, Felix and Wiegand, Thorsten},
-doi = {10.1111/jvs.12313},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vel{\'{a}}zquez et al. - 2015 - Linking trait similarity to interspecific spatial associations in a moist tropical forest.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {1068--1079},
-title = {{Linking trait similarity to interspecific spatial associations in a moist tropical forest}},
-url = {http://doi.wiley.com/10.1111/jvs.12313},
-volume = {26},
-year = {2015}
-}
-@article{Granger2015,
-abstract = {* Mapping diversity indices, that is estimating values in all locations of a given area from some sampled locations, is central to numerous research and applied fields in ecology. * Two approaches are used to map diversity indices without including abiotic or biotic variables: (i) the indirect approach, which consists in estimating each individual species distribution over the area, then stacking the distributions of all species to estimate and map a posteriori the diversity index, (ii) the direct approach, which relies on computing a diversity index in each sampled locations and then to interpolate these values to all locations of the studied area for mapping. * For both approaches, we document drawbacks from theoretical and practical viewpoints and argue about the need for adequate interpolation methods. First, we point out that the indirect approach is problematic because of the high proportion of rare species in natural communities. This leads to zero-inflated distributions, which cannot be interpolated using standard statistical approaches. Secondly, the direct approach is inaccurate because diversity indices are not spatially additive, that is the diversity of a studied area (e.g. region) is not the sum of the local diversities. Therefore, the arithmetic variance and some of its derivatives, such as the variogram, are not appropriate to ecologically measure variation in diversity indices. For the direct approach, we propose to consider the $\beta$-diversity, which quantifies diversity variations between locations, by the mean of a $\beta$-gram within the interpolation procedure. We applied this method, as well as the traditional interpolation methods for comparison purposes on different faunistic and floristic data sets collected from scientific surveys. We considered two common diversity indices, the species richness and the Rao's quadratic entropy, knowing that the above issues are true for complementary species diversity indices as well as those dealing with other biodiversity levels such as genetic diversity. * We conclude that none of the approaches provided an accurate mapping of diversity indices and that further methodological developments are still needed. We finally discuss lines of research that may resolve this key issue, dealing with conditional simulations and models taking into account biotic and abiotic explanatory variables.},
-author = {Granger, Victoria and Bez, Nicolas and Fromentin, Jean-Marc and Meynard, Christine and Jadaud, Ang{\'{e}}lique and M{\'{e}}rigot, Bastien},
-doi = {10.1111/2041-210X.12357},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Granger et al. - 2015 - Mapping diversity indices not a trivial issue.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {6},
-pages = {688--696},
-title = {{Mapping diversity indices: not a trivial issue}},
-url = {http://dx.doi.org/10.1111/2041-210X.12357{\%}5Cnhttp://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12357/abstract},
-volume = {6},
-year = {2015}
-}
-@book{Manly1991,
-address = {London},
-author = {Manly, B. F.},
-publisher = {Chapman and Hall},
-title = {{Randomization and Monte-Carlo methods in biology}},
-year = {1991}
-}
-@article{Grabchak2016,
-abstract = {Modern measures of diversity satisfy reasonable axioms, are parameterized to produce diversity profiles, can be expressed as an effective number of species to simplify their interpretation, and come with estimators that allow one to apply them to real-world data. We introduce the generalized Simpson's entropy as a measure of diversity and investigate its properties. We show that it has many useful features and can be used as a measure of biodiversity. Moreover, unlike most commonly used diversity indices, it has unbiased estimators, which allow for sound estimation of the diversity of poorly sampled, rich communities.},
-author = {Grabchak, Michael and Marcon, Eric and Lang, Gabriel and Zhang, Zhiyi},
-doi = {10.1371/journal.pone.0173305},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grabchak et al. - 2017 - The Generalized Simpson's Entropy is a Measure of Biodiversity.pdf:pdf},
-journal = {Plos One},
-number = {3},
-pages = {e0173305},
-title = {{The Generalized Simpson's Entropy is a Measure of Biodiversity}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173305},
-volume = {12},
-year = {2017}
-}
-@article{Gosselin2011,
-abstract = {Recent approaches mixing frequentist principles with bayesian inference propose internal goodness-of-fit (GOF) p-values that might be valuable for critical analysis of bayesian statistical models. However, GOF p-values developed to date only have known probability distributions under restrictive conditions. As a result, no known GOF p-value has a known probability distribution for any discrepancy function.},
-author = {Gosselin, Fr{\'{e}}d{\'{e}}ric},
-doi = {10.1371/journal.pone.0014770},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gosselin - 2011 - A new calibrated bayesian internal goodness-of-fit method Sampled posterior p-values as simple and general p-values th.pdf:pdf},
-journal = {PLoS ONE},
-number = {3},
-pages = {e14770},
-title = {{A new calibrated bayesian internal goodness-of-fit method: Sampled posterior p-values as simple and general p-values that allow double use of the data}},
-volume = {6},
-year = {2011}
-}
-@article{Paine2015,
-abstract = {1. Functional traits provide insight into a variety of ecological questions, yet the optimal sam- pling method to estimate the community-level distribution of plant functional trait values remains a subject of debate, especially in species-rich forests. 2. We present a simulation analysis of the trait distribution of a set of nine completely sampled permanent plots in the lowland rain forests of French Guiana. 3. Increased sampling intensity consistently improved accuracy in estimating community- weighted means and variances of functional trait values, whereas there was substantial varia- tion among functional traits and minor differences among sampling strategies. 4. Thus, investment in intensified sampling yields a greater improvement in the accuracy of estimation than does an equivalent investment in sampling design complication. 5. Notably, ‘taxon-free' strategies frequently had greater accuracy than did abundance-based strategies, which had the additional cost of requiring botanical surveys. 6. We conclude that there is no substitute for extensive field sampling to accurately character- ize the distribution of functional trait values in species-rich forests.},
-author = {Paine, C. E. Timothy and Baraloto, Christopher and D{\'{i}}az, Sandra},
-doi = {10.1111/1365-2435.12433},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Paine, Baraloto, D{\'{i}}az - 2015 - Optimal strategies for sampling functional traits in species-rich forests.pdf:pdf},
-journal = {Functional Ecology},
-number = {10},
-pages = {1325--1331},
-title = {{Optimal strategies for sampling functional traits in species-rich forests}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12433/abstract},
-volume = {29},
-year = {2015}
-}
-@article{Shimadzu2016,
-abstract = {Every ecological data set is the result of sampling the biota at sampling locations. Such samples are rarely a census of the biota at the sampling locations and so will inherently contain biases. It is crucial to account for the bias induced by sampling if valid inference on biodiversity quantities is to be drawn from the observed data. The literature on accounting for sampling effects is large, but most are dedicated to the specific type of inference required, the type of analysis performed and the type of survey undertaken. There is no general and systematic approach to sampling. Here, we explore the unification of modelling approaches to account for sampling. We focus on individuals in ecological communities as the fundamental sampling element, and show that methods for accounting for sampling at the species level can be equated to individual sampling effects. Particular emphasis is given to the case where the probability of observing an individual, when it is present at the site sampled, is less than one. We call these situations ‘imperfect observations'. The proposed framework is easily implemented in standard software packages. We highlight some practical benefits of this formal framework: the ability of predicting the true number of individuals using an expectation that conditions on the observed data, and designing appropriate survey plans accounting for uncertainty due to sampling. The principles and methods are illustrated with marine survey data from tropical northern Australia.},
-author = {Shimadzu, Hideyasu and Foster, Scott D. and Darnell, Ross},
-doi = {10.1007/s10651-016-0342-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shimadzu, Foster, Darnell - 2016 - Imperfect observations in ecological studies.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {3},
-pages = {337--358},
-title = {{Imperfect observations in ecological studies}},
-url = {http://link.springer.com/10.1007/s10651-016-0342-2},
-volume = {23},
-year = {2016}
-}
-@article{Moreno2010,
-abstract = {There is a genuine need for consensus on a clear terminology in the study of species diversity given that the nature of the components of diversity is the subject of an ongoing debate and may be the key to understanding changes in ecosystem processes. A recent and thought-provoking paper (Jurasinski et al. Oecologia 159:15-26, 2009) draws attention to the lack of precision with which the terms alpha, beta, and gamma diversity are used and proposes three new terms in their place. While this valuable effort may improve our understanding of the different facets of species diversity, it still leaves us far from achieving a consistent terminology. As such, the conceptual contribution of these authors is limited and does little to elucidate the facets of species diversity. It is, however, a good starting point for an in-depth review of the available concepts and methods.},
-author = {Moreno, Claudia E. and Rodr{\'{i}}guez, Pilar},
-doi = {10.1007/s00442-010-1591-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moreno, Rodr{\'{i}}guez - 2010 - A consistent terminology for quantifying species diversity.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {279--82},
-title = {{A consistent terminology for quantifying species diversity?}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/20213149},
-volume = {163},
-year = {2010}
-}
-@article{Zahl1977,
-abstract = {The method of jackknifing is introduced for estimating an index of diversity and is illustrated with tree data. The method yields approximately normally distributed jackknife estimates and also gives estimated standard deviations, making possible tests of hypotheses and confidence interval estimates. These results apparently can be obtained under the usual conditions of field sampling, where associations within and between species or between quadrats or segments of a traverse may be found. Because of these associations there is no guarantee that the method works; hence an eyball and a statistical test for the approximate normality of the estimates are given and illustrated with the tree data. The tree data come from 24 quadrats arranged in two blocks of contiguous quadrats. The estimated tree-species diversity, using both indices considered, showed a smooth monotonic decrease over a 19-yr interval providing striking confirmation of the reality of this ecological parameter. The normality tests on this data showed that the normal approximations to the distributions of the jackknife estimates were justified, except in three instances, only one of which seemed to be seriously in error. A conclusion is that it seems reasonable to suppose that in many, if not most, cases, only moderate sample sizes will be needed in practice for the jackknife estimate, at least for forest data.},
-author = {Zahl, Samuel},
-doi = {10.2307/1936227},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zahl - 1977 - Jackknifing An Index of Diversity.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {907--913},
-title = {{Jackknifing An Index of Diversity}},
-url = {http://www.jstor.org/stable/1936227},
-volume = {58},
-year = {1977}
-}
-@techreport{Sabatier1982,
-address = {Paris},
-author = {Sabatier, Daniel and Puig, Henri},
-publisher = {Mus{\'{e}}um National d'Histoire Naturelle},
-title = {{Ph{\'{e}}nologie et saisonnalit{\'{e}} de la floraison et de la fructification en for{\^{e}}t dense guyanaise}},
-year = {1982}
-}
-@article{Benton2013a,
-abstract = {Biodiversity today is huge, and it has a long history. Identifying rules for the heterogeneity of modern biodiversity-the high to low species richness of different clades-has been hard. There are measurable biodiversity differences between land and sea and between the tropics and temperate-polar regions. Some analyses suggest that the net age of a clade can determine its extinction risk, but this is equivocal. New work shows that, through geological time, clades pass through different diversification regimes, and those regimes constrain the balance of tree size and the nature of branching events.},
-author = {Benton, Michael J.},
-doi = {10.1111/pala.12012},
-journal = {Palaeontology},
-number = {1},
-pages = {1--7},
-title = {{Origins of biodiversity}},
-volume = {56},
-year = {2013}
-}
-@article{Chesson1994,
-abstract = {A general model of competition between several species in a variable environment is presented and analyzed using a general method that unifies treatment of different specific models. This method yields broad conclusions that are independent of the details of a model. It is used here to show that mechanisms of coexistence and competitive exclusion are largely restricted to three broad categories. One of these categories includes classical mechanisms that do not depend on fluctuations over time. Another category includes mechanisms which may be referred to collectively as the storage effect. These mechanisms involve species-specific responses to environmental fluctuations, a relationship between fluctuations in competition and fluctuations in the environment, and an interaction between environment and competition. The final category depends on fluctuating competition and nonlinear responses to competition that differ between species. These general results are illustrated with analyses of several specific models, including a Lotka-Volterra model, a model of nonlinear resource consumption, and models of recruitment fluctuations for iteroparous organisms and for annual plants.},
-author = {Chesson, P.},
-doi = {10.1006/tpbi.1994.1013},
-isbn = {0040-5809},
-issn = {00405809},
-journal = {Theoretical Population Biology},
-number = {3},
-pages = {227--276},
-pmid = {199497416278},
-title = {{Multispecies Competition in Variable Environments}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580984710136},
-volume = {45},
-year = {1994}
-}
-@article{McCain2016,
-abstract = {Aim Studies of species turnover commonly assume that turnover is a critical determinant of species richness patterns. But the concordance in patterns of turnover and species richness along gradients is poorly known. Here we characterize elevational patterns of species turnover and test whether turnover and species richness are strongly related. Location Sixty-two elevation gradients world-wide, from 17° S to 43° N. Methods We used elevational range data for six terrestrial vertebrate groups to characterize species turnover between neighbouring elevational bands. We measured turnover as Simpson's dissimilarity, a metric that is unaffected by measured differences in species richness among recorded samples. To assess differences from random patterns, elevational turnover was compared with three null models (hard, soft and no boundaries). Lastly, elevational turnover was compared with the combined species richness of neighbouring elevational bands. Analyses were conducted at three grain sizes (200, 400 and 800 m elevation). Results We found no consistent, repeated patterns in elevational turnover. Variability among gradients was very high, with most datasets displaying multiple but inconsistently located peaks. Concordance between null predictions and empirical turnover was poor (average r2 for 200, 400 and 800m grains were: hard boundaries 0.06, 0.12 and 0.15; soft boundaries 0.06, 0.11 and 0.14; unbounded 0.03, 0.07 and 0.10; respectively), although many empirical values fell within the confidence intervals of the null model. Correlations of turnover and species richness were generally poor, but increased with analysis grain (average r2 = 0.19, 0.33 and 0.54, respectively). Main conclusions Turnover cannot serve as a general explanation for richness patterns within elevational gradients. Elevational turnover patterns are highly idiosyncratic, change with scale, and are often indistinguishable from random patterns. Despite the common assertion that the highest species richness occurs where distinct, dominant communities turn over on mountains (e.g. low- and high-elevation communities at a middle ecotone), we found no strong support for such Clementsian-structured patterns.},
-author = {McCain, Christy M. and Beck, Jan},
-doi = {10.1111/geb.12410},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McCain, Beck - 2016 - Species turnover in vertebrate communities along elevational gradients is idiosyncratic and unrelated to species r.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {3},
-pages = {299--310},
-title = {{Species turnover in vertebrate communities along elevational gradients is idiosyncratic and unrelated to species richness}},
-url = {http://doi.wiley.com/10.1111/geb.12410},
-volume = {25},
-year = {2016}
-}
-@article{Sarkar2002,
-author = {Sarkar, Sahotra},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sarkar - 2002 - Defining Biodiversity Assessing Biodiversity.pdf:pdf},
-journal = {The Monist},
-number = {1},
-pages = {131--155},
-title = {{Defining "Biodiversity"; Assessing Biodiversity}},
-volume = {85},
-year = {2002}
-}
-@article{Rull2008,
-abstract = {The evolutionary origin of extant species in the Neotropics, one of the most biodiverse regions of the world, has been widely debated. One hypothesis is that neotropical species emerged primarily during the Quaternary (the last approximately 2 million years), favoured by alternating glacial/interglacial climates. An opposite view proposes an older Tertiary origin linked primarily to palaeogeographical changes. Here, a thorough review of the available literature on DNA molecular dating shows that the Tertiary-Quaternary debate no longer makes sense. Indeed, the {\textgreater} 1400 neotropical species whose origin has been dated have appeared in a continual fashion since the late Eocene/early Oligocene (approximately 39 million years before present) to the Quaternary. Palaeogeographical mechanisms of speciation are relatively well accepted, but diversification processes linked to climate are still controversial. These results are important to unravel both the origin of present-day biodiversity patterns at both local and global scales and the genetic and environmental mechanisms involved, which are two crucial aspects for suitable biodiversity conservation strategies.},
-author = {Rull, Valent{\'{i}}},
-doi = {10.1111/j.1365-294X.2008.03789.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rull - 2008 - Speciation timing and neotropical biodiversity The Tertiary-Quaternary debate in the light of molecular phylogenetic evide.pdf:pdf},
-journal = {Molecular Ecology},
-number = {11},
-pages = {2722--2729},
-title = {{Speciation timing and neotropical biodiversity: The Tertiary-Quaternary debate in the light of molecular phylogenetic evidence}},
-volume = {17},
-year = {2008}
-}
-@article{Dark2004,
-abstract = {The spatial distribution of invasive alien plants has been poorly documented in California. However, with the increased availability of GIS software and spatially explicit data, the distribution of invasive alien plants can be explored. Using bioregions as defined in Hickman (1993), I compared the distribution of invasive alien plants (n = 78) and noninvasive alien plants (n = 1097). The distribution of both categories of alien plants was similar with the exception of a higher concentration of invasive alien plants in the North Coast bioregion. Spatial autocorrelation analysis using Moran's I indicated significant spatial dependence for both invasive and noninvasive alien plant species. I used both ordinary least squares (OLS) and spatial autoregressive (SAR) models to assess the relationship between alien plant species distribution and native plant species richness, road density, population density, elevation, area of sample unit, and precipitation. The OLS model for invasive alien plants included two significant effects; native plant species richness and elevation. The SAR model for invasive alien plants included three significant effects; elevation, road density, and native plant species richness. The SAR model for noninvasive alien plants resulted in the same significant effects as invasive alien plants. Both invasive and noninvasive alien plants are found in regions with low elevation, high road density, and high native-plant species richness. This is in congruity with previous spatial pattern studies of alien plant species. However, the similarity in effects for both categories of alien plants alludes to the importance of autecological attributes, such as pollination system, dispersal system and differing responses to disturbance in the distribution of invasive plant species. In addition, this study emphasizes the critical importance of testing for spatial autocorrelation in spatial pattern studies and using SAR models when appropriate.},
-annote = {Article},
-author = {Dark, Shawna J.},
-doi = {10.1111/j.1472-4642.2004.00054.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dark - 2004 - The biogeography of invasive alien plants in California an application of GIS and spatial regression analysis.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {1},
-pages = {1--9},
-title = {{The biogeography of invasive alien plants in California: an application of GIS and spatial regression analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2004.00054.x/abstract},
-volume = {10},
-year = {2004}
-}
-@article{Marcon2014b,
-abstract = {Measuring functional or phylogenetic diversity is the object of an active literature. The main issues to address are relating measures to a clear conceptual framework, allowing unavoidable estimation-bias correction and decomposing diversity along spatial scales. We provide a general mathematical framework to decompose measures of species-neutral, phylogenetic or functional diversity into $\alpha$ and $\beta$ components. We first unify the definitions of phylogenetic and functional entropy and diversity as a generalization of HCDT entropy and Hill numbers when an ultrametric tree is considered. We then derive the decomposition of diversity. We propose a bias correction of the estimates allowing meaningful computation from real, often undersampled communities. Entropy can be transformed into true diversity, that is an effective number of species or communities. Estimators of $\alpha$- and $\beta$-entropy, phylogenetic and functional entropy are provided. Proper definition and estimation of diversity is the first step towards better understanding its underlying ecological and evolutionary mechanisms.},
-author = {Marcon, Eric and H{\'{e}}rault, Bruno},
-doi = {10.1111/2041-210X.12323},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, H{\'{e}}rault - 2015 - Decomposing Phylodiversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {333--339},
-title = {{Decomposing Phylodiversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12323/abstract},
-volume = {6},
-year = {2015}
-}
-@article{Janzen1971,
-abstract = {A review of literature, discussing seed and fruit consumption by animals (both vertebrate and invertebrate) before and after seed dispersal, the role of such animals in seed dispersal, effects of plant-chemical and related factors, etc. A section is devoted to the role of seed- and fruit-consuming animals in modifying forest composition.},
-author = {Janzen, D H},
-doi = {10.1146/annurev.es.02.110171.002341},
-isbn = {0066-4162},
-issn = {0066-4162},
-journal = {Annual Review of Ecology and Systematics},
-number = {1},
-pages = {465--492},
-pmid = {9474},
-title = {{Seed Predation by Animals}},
-url = {http://www.annualreviews.org/doi/10.1146/annurev.es.02.110171.002341},
-volume = {2},
-year = {1971}
-}
-@article{Duncan1991,
-abstract = {(1) The importance of intra- and interspecific competition in affecting the growth and survival of Dacrycarpus dacrydioides and Dacrydium cupressinum, the two dominant trees in a mixed podocarp stand in Ohinemaka Forest, south Westland, New Zealand, was investigated. Two lines of evidence (spatial patterning of trees and correlates of tree performance with neighbourhood density) were used to infer the importance of competition. (2) Intraspecific competition among D. dacrydioides trees appeared to be intense. Mean radial growth rate (MGR) was significantly negatively correlated with the number of conspecific neighbours, and patterns of non-random mortality resulted in a shift in spatial pattern from a significantly clumped to a significantly regular distribution. In contrast, intraspecific competition among D. cupressinum was less intense. D. cupressinum had a low rate of mortality, predominatly random spatial patterns of mortality, and a weak correlation between MGR and the number of conspecific neighbours. (3) Differences in the relative importance of intraspecific competition in affecting survival and growth of the two species was attributed to differences in the distribution and availability of suitable establishment sites. D. dacrydioides preferentially established on abundant level or slightly elevated sites, and in patches reached densities where resources were limiting. In contrast, the number and distribution of D. cupressinum were determined primarily by the availability of suitable elevated establishment sites that were scattered throughout the stand. The restricted number of suitable sites limited D. cupressinum to densities where resources were not severely limiting. (4) There was no evidence of interspecific competition. Rather the two species avoided interspecific competition by partitioning the variability in forest-floor micro-relief. Partitioning of sites may permit the coexistence of the two species.},
-author = {Duncan, Richard P.},
-doi = {10.2307/2261099},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duncan - 1991 - Competition and the coexistence of species in a mixed podocarp stand.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {1073--1084},
-title = {{Competition and the coexistence of species in a mixed podocarp stand}},
-url = {https://www.jstor.org/stable/2261099},
-volume = {79},
-year = {1991}
-}
-@book{Pielou1975,
-address = {New York},
-author = {Pielou, Evelyn C.},
-isbn = {0471689254},
-publisher = {Wiley},
-title = {{Ecological Diversity}},
-year = {1975}
-}
-@article{Jaffe1993,
-abstract = {We compare the geographic location of patent citations with that of the cited patents, as evidence of the extent to which knowledge spillovers are geographically localized. We find that citations to domestic patents are more likely to be domestic, and more likely to come from the same state and SMSA as the cited patents, compared with a “control frequency” reflecting the pre-existing concentration of related research activity. These effects are particularly significant at the local (SMSA) level. Localization fades over time, but only very slowly. There is no evidence that more “basic” inventions diffuse more rapidly than others.},
-author = {Jaffe, Adam B. and Trajtenberg, Manuel and Henderson, Rebecca},
-doi = {10.2307/2118401},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaffe, Trajtenberg, Henderson - 1993 - Geographical Localization of Knowledge Spillovers as Evidenced by Patent Citations.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {3},
-pages = {577--598},
-title = {{Geographical Localization of Knowledge Spillovers as Evidenced by Patent Citations}},
-url = {https://doi.org/10.2307/2118401},
-volume = {108},
-year = {1993}
-}
-@article{Mayer1975,
-author = {Mayer, Wolfgang and Pleeter, Saul},
-doi = {10.1016/0166-0462(75)90030-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mayer, Pleeter - 1975 - A Theoretical Justification for the Use of Location Quotients.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {3},
-pages = {343--355},
-title = {{A Theoretical Justification for the Use of Location Quotients}},
-url = {http://www.sciencedirect.com/science/article/pii/0166046275900307},
-volume = {5},
-year = {1975}
-}
-@article{Pielou1966a,
-abstract = {Information content may be used as a measure of the diversity of a many-species biological collection. The diversity of small collections, all of whose members can be identified and counted, is defined by Brillouin's measure of information. With larger collections it becomes necessary to estimate diversity; what is estimated is Shannon's measure of information which is a function of the population proportions of the several species. Different methods of estimation are appropriate for different types of collections. If the collection can be randomly sampled and the total number of species is known, Basharin's formula may be used. With a random sample from a population containing an unknown number of species, Good's method is sometimes applicable. With a patchy population of sessile organisms, such as a plant community, random samples are unobtainable since the contents of a randomly placed quadrat are not a random sample of the parent population. To estimate the diversity of such a community a method is proposed whereby the sample size is progressively increased by addition of new quadrats; as this is done the diversity of the pooled sample increases and then levels off. The mean increment in total diversity that results from enlarging the sample still more then provides an estimate of the diversity per individual in the whole population. {\textcopyright} 1966.},
-annote = {Cited By (since 1996): 746
-Export Date: 24 January 2012
-Source: Scopus},
-author = {Pielou, Evelyn C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1966 - The measurement of diversity in different types of biological collections.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {C},
-pages = {131--144},
-title = {{The measurement of diversity in different types of biological collections}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0009752612{\&}partnerID=40{\&}md5=f7ea2eceb9bbbd17a478a1ec6d15eb81},
-volume = {13},
-year = {1966}
-}
-@book{Hardy1952,
-author = {Hardy, G. H. and Littlewood, J. E. and P{\'{o}}lya, G.},
-isbn = {9780521358804},
-publisher = {Cambridge University Press},
-title = {{Inequalities}},
-url = {http://books.google.com/books?id=t1RCSP8YKt8C},
-year = {1952}
-}
-@article{Corona2011,
-abstract = {Statistically-designed inventories and biodiversity monitoring programs are gaining relevance for biological conservation and natural resources management. Mandated periodic surveys provide unique opportunities to identify and satisfy natural resources management information needs. However, this is not an end in itself but rather is the beginning of a process that should lead to sound decision-making in biodiversity conservation. Forest inventories are currently evolving towards multipurpose resource surveys and are broadening their scope in several directions: (i) expansion of the target population to include non-traditional attributes such as trees outside the forest and urban forests; (ii) forest carbon pools and carbon sequestration estimation; (iii) assessment of forest health; and (iv) inclusion of additional variables such as biodiversity attributes that are not directly related to timber assessment and wood harvesting.There is an on-going debate regarding the role of forest inventories in biodiversity assessment and monitoring. This paper presents a review on the topic that aims at providing updated knowledge on the current contribution of forest inventories to the assessment and monitoring of forest biodiversity conditions on a large scale. Specific objectives are fourfold: (i) to highlight the types of forest biodiversity indicators that can be estimated from data collected in the framework of standard forest inventories and the implications of different sampling methods on the estimation of the indicators; (ii) to outline current possibilities for harmonized estimation of biodiversity indicators in Europe from National Forest Inventory data; (iii) to show the added value for forest biodiversity monitoring of framing biodiversity indicators into ecologically meaningful forest type units; and (iv) to examine the potential of forest inventory sample data for estimating landscape biodiversity metrics. ?? 2011 Elsevier B.V.},
-author = {Corona, Piermaria and Chirici, Gherardo and McRoberts, Ronald E. and Winter, Susanne and Barbati, Anna},
-doi = {10.1016/j.foreco.2011.08.044},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Corona et al. - 2011 - Contribution of large-scale forest inventories to biodiversity assessment and monitoring.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {11},
-pages = {2061--2069},
-title = {{Contribution of large-scale forest inventories to biodiversity assessment and monitoring}},
-url = {http://dx.doi.org/10.1016/j.foreco.2011.08.044},
-volume = {262},
-year = {2011}
-}
-@article{Clark2010,
-abstract = {High biodiversity of forests is not predicted by traditional models, and evidence for trade-offs those models require is limited. High-dimensional regulation (e.g.. N factors to regulate N species) has long been recognized as a possible alternative explanation, but it has not be been seriously pursued, because only a few limiting resources are evident for trees, and analysis of multiple interactions is challenging. We develop a hierarchical model that allows us to synthesize data from long-term, experimental; data sets with processes that control growth, maturation, fecundity, and survival. We allow for uncertainty at all stages and variation among 26 000 individuals and over time, including 268 000 tree years, for dozens of tree species. We estimate population-level parameters that apply at the species level and the interactions among latent states, i.e., the demographic rates for each individual, every year. The former show that the traditional trade-offs used to explain diversity are not present. Demographic rates overlap among species, and they do not show trends consistent with maintenance of diversity by simple mechanisms (negative correlations and limiting similarity). However, estimates of latent states at the level of individuals and years demonstrate that species partition environmental variation. Correlations between responses to variation in time are high for individuals of the same species, but not for individuals of different species. We demonstrate that these relationships are pervasive, providing strong evidence that high-dimensional regulation is critical for biodiversity regulation.},
-annote = {ISI Document Delivery No.: 671CY
-Times Cited: 38
-Cited Reference Count: 166
-Clark, James S. Bell, David Chu, Chengjin Courbaud, Benoit Dietze, Michael Hersh, Michelle HilleRisLambers, Janneke Ibanez, Ines LaDeau, Shannon McMahon, Sean Metcalf, Jessica Mohan, Jacqueline Moran, Emily Pangle, Luke Pearson, Scott Salk, Carl Shen, Zehao Valle, Denis Wyckoff, Peter
-Nsf [bsr-9444146, deb 9453498, deb-9632854, deb-9981392, idea-0308498, deb 0425465, seii 0430693, dddas 0540347]
-Field, lab, and remote sensing involved a large number of undergraduates and research technicians, including Nathan Buchanan, Melissa Burt, Alyssa Cooper, Natalia Dorfman, Maryana Draga, Amy Hamilton, Saida Ismayilova, Amber Loucks, Allen McBride, Lauren Nichols, Clint Oakley, Luke Pangle, Danielle Racke, Quentin Read, Sarah Rorick, Greta Schmoyer, Jason Styons, Emily White, Miranda Welsh, Jamie West, John Williamson, and Nathan Welch. We thank Maria Uriarte and three anonymous reviewers for comments on the manuscript. The research was supported by NSF grants BSR-9444146, DEB 9453498, DEB-9632854, DEB-9981392, IDEA-0308498, DEB 0425465, SEII 0430693, and DDDAS 0540347 and by several Dissertation Improvement Grants.
-Ecological soc amer
-Washington},
-author = {Clark, James S. and Bell, David and Chu, Chengjin and Courbaud, Beno{\^{i}}t and Dietze, Michael and Hersh, Michelle and HilleRisLambers, Janneke and Ibanez, In{\'{e}}s and LaDeau, Shannon and McMahon, Sean and Metcalf, Jessica and Mohan, Jacqueline and Moran, Emily and Pangle, Luke and Pearson, Scott and Salk, Carl and Shen, Zehao and Valle, Denis and Wyckoff, Peter},
-doi = {10.1890/09-1541.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clark et al. - 2010 - High-dimensional coexistence based on individual variation a synthesis of evidence.pdf:pdf},
-journal = {Ecological Monographs},
-number = {4},
-pages = {569--608},
-title = {{High-dimensional coexistence based on individual variation: a synthesis of evidence}},
-volume = {80},
-year = {2010}
-}
-@book{Foret2006,
-author = {For{\^{e}}t, R.},
-isbn = {9782804152482},
-publisher = {De Boeck},
-title = {{Dico de Bio}},
-url = {http://books.google.fr/books?id=egTUUixxdNcC},
-year = {2006}
-}
-@incollection{Casetta2014a,
-abstract = {Si l'on regarde {\`{a}} la naissance du mot biodiversit{\'{e}}, les esp{\`{e}}ces jouent un r{\^{o}}le fondamental. N{\'{e}}anmoins, la notion d'esp{\`{e}}ce est difficile {\`{a}} cerner – au point que dans la litt{\'{e}}rature on parle d'un v{\'{e}}ritable « probl{\`{e}}me de l'esp{\`{e}}ce » – et plusieurs auteurs ont sugg{\'{e}}r{\'{e}} de l'abandonner. Ce chapitre vise {\`{a}} d{\'{e}}fendre l'utilit{\'{e}} de la notion d'esp{\`{e}}ce par rapport {\`{a}} l'{\'{e}}valuation et {\`{a}} la conservation de la biodiversit{\'{e}} en prenant en consid{\'{e}}ration les difficult{\'{e}}s que les d{\'{e}}tracteurs de la notion soulignent – tout particuli{\`{e}}rement l'objection selon laquelle la biodiversit{\'{e}} ne serait pas les esp{\`{e}}ces et le d{\'{e}}saccord sur le comptage des esp{\`{e}}ces r{\'{e}}sultant du pluralisme taxinomique. Dans le premier cas, on montre que l'objection rate sa cible ; dans le second cas, on sugg{\`{e}}re {\`{a}} l'aide d'une {\'{e}}tude de cas que le d{\'{e}}saccord est plus substantiel mais aussi qu'il peut {\^{e}}tre circonvenu.},
-address = {Paris},
-author = {Casetta, Elena},
-booktitle = {La biodiversit{\'{e}} en question. Enjeux philosophiques, {\'{e}}thiques et scientifiques},
-chapter = {5},
-editor = {Casetta, Elena and Delord, Julien},
-pages = {139--154},
-publisher = {Editions Mat{\'{e}}riologiques},
-title = {{{\'{E}}valuer et conserver la biodiversit{\'{e}} face au probl{\`{e}}me des esp{\`{e}}ces}},
-year = {2014}
-}
-@article{Zanne2014,
-abstract = {Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.},
-author = {Zanne, Amy E. and Tank, David C. and Cornwell, William K. and Eastman, Jonathan M. and Smith, Stephen A. and FitzJohn, Richard G. and McGlinn, Daniel J. and O'Meara, Brian C. and Moles, Angela T. and Reich, Peter B. and Royer, Dana L. and Soltis, Douglas E. and Stevens, Peter F. and Westoby, Mark and Wright, Ian J. and Aarssen, Lonnie W. and Bertin, Robert I. and Calaminus, Andre and Govaerts, Rafa{\"{e}}l and Hemmings, Frank and Leishman, Michelle R. and Oleksyn, Jacek and Soltis, Pamela S. and Swenson, Nathan G. and Warman, Laura and Beaulieu, Jeremy M.},
-doi = {10.1038/nature12872},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zanne et al. - 2014 - Three keys to the radiation of angiosperms into freezing environments.pdf:pdf},
-journal = {Nature},
-number = {7486},
-pages = {89--92},
-title = {{Three keys to the radiation of angiosperms into freezing environments}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/24362564},
-volume = {506},
-year = {2014}
-}
-@article{Taubert2015,
-abstract = {The search for simple principles underlying the complex architecture of ecological communities such as forests still challenges ecological theorists. We use tree diameter distributions—fundamental for de- riving other forest attributes—to describe the structure of tropical forests. Here we argue that tree diameter distributions of natural tropical forests can be explained by stochastic packing of tree crowns representing a forest crown packing system: a method usu- ally used in physics or chemistry. We demonstrate that tree diame- ter distributions emerge accurately from a surprisingly simple set of principles that include site-specific tree allometries, random place- ment of trees, competition for space, and mortality. The simple static model also successfully predicted the canopy structure, re- vealing that most trees in our two studied forests grow up to 30– 50 m in height and that the highest packing density of about 60{\%} is reached between the 25- and 40-m height layer. Our approach is an important step toward identifying a minimal set of processes. responsible for generating the spatial structure of tropical forests},
-author = {Taubert, Franziska and Jahn, Markus Wilhelm and Dobner, Hans-J{\"{u}}rgen and Wiegand, Thorsten and Huth, Andreas},
-doi = {10.1073/pnas.1513417112},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Taubert et al. - 2015 - The structure of tropical forests and sphere packings.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {49},
-pages = {15125--15129},
-title = {{The structure of tropical forests and sphere packings}},
-url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1513417112},
-volume = {112},
-year = {2015}
-}
-@article{Ricotta2003c,
-abstract = {Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs.},
-author = {Ricotta, Carlo and Avena, Giancarlo C.},
-doi = {10.1023/A:1023000322071},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Avena - 2003 - An information-theoretical measure of taxonomic diversity.pdf:pdf},
-journal = {Acta biotheoretica},
-number = {51},
-pages = {35--41},
-title = {{An information-theoretical measure of taxonomic diversity}},
-url = {http://link.springer.com/article/10.1023/A:1023000322071},
-volume = {25},
-year = {2003}
-}
-@article{Garnier1999,
-abstract = {The relationships between leaf structure, nitrogen concentration and CO2 assimilation rate (A) were studied for 14 grass species grown in the laboratory under non-limiting nutrient conditions. Structural features included leaf thickness and density, and the proportion of leaf volume occupied by different types of tissue (mesophyll, epidermis, vessels and sclerenchyma). Relationships were assessed for data expressed per unit leaf area and fresh mass. The latter was found to be closely related to leaf volume, which allowed us to use A per unit leaf fresh mass (Afm) as a surrogate of A per unit leaf volume. Assimilation rate per unit leaf area (Aa) was positively correlated with leaf thickness and with the amount of mesophyll per unit leaf area; the relationship with leaf nitrogen content per unit area was only marginally significant. Afm was negatively correlated with leaf thickness and positively with fresh mass-based leaf organic nitrogen concentration. A multiple regression involving these two variables explained 81{\%} of the variance in Afm. The value of Afm was also significantly related to the proportion of mesophyll in the leaf volume, but surprisingly the correlation was negative. This was because thin leaves with high Afm and nitrogen concentration had proportionally more mechanically supportive tissues than thick ones; as a consequence, they also had a lower proportion of mesophyll. These data suggest that, in addition to leaf nitrogen, leaf thickness has a strong impact on CO2 assimilation rate for the grass species studied.},
-author = {Garnier, Eric and Salager, J. L. and Laurent, G. and Soni{\'{e}}, L.},
-doi = {10.1046/j.1469-8137.1999.00426.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garnier et al. - 1999 - Relationships between photosynthesis, nitrogen and leaf structure in 14 grass species and their dependence on th.pdf:pdf},
-journal = {New Phytologist},
-number = {1},
-pages = {119--129},
-title = {{Relationships between photosynthesis, nitrogen and leaf structure in 14 grass species and their dependence on the basis of expression}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1469-8137.1999.00426.x/full},
-volume = {143},
-year = {1999}
-}
-@article{Bengtsson1998,
-abstract = {I examine a number of problems that need to be identified and accounted for when examining the relationships between diversity and ecosystem function. Among these are measures of diversity and complexity in ecosystems: species richness, diversity indices, functional groups, keystone species, connectance, etc, all of which may be difficult to relate to ecosystem function. Several important distinctions, when testing diversity-function relationships empirically, are discussed: Diversity of functional groups, diversity within functional groups vs, total diversity; manipulating variables such as body-size distributions vs. manipulating diversity per se; effects of diversity vs. effects of biomass; and diversity-function relations under stable vs. changing conditions or perturbations. It is argued that for the management and development of sustainable ecosystems, it is probably more important to understand the Linkages between key species or functional groups and ecosystem function, rather than focusing on species diversity. This is because there are possible mechanistic relations between what species do in ecosystems and ecosystem function. Diversity, being an abstract and aggregated property of the species in the context of communities and ecosystems, lacks such direct relations to ecosystem functions. (C) 1998 Elsevier Science B.V.},
-author = {Bengtsson, J.},
-doi = {10.1016/S0929-1393(98)00120-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bengtsson - 1998 - Which species What kind of diversity Which ecosystem function Some problems in studies of relations between biodivers.pdf:pdf},
-journal = {Applied Soil Ecology},
-number = {3},
-pages = {191--199},
-title = {{Which species? What kind of diversity? Which ecosystem function? Some problems in studies of relations between biodiversity and ecosystem function}},
-url = {http://www.sciencedirect.com/science/article/pii/S0929139398001206},
-volume = {10},
-year = {1998}
-}
-@article{Byers1992,
-abstract = {1. Algorithms for Dirichlet tessellation of spatial points are developed and implemented on personal computer. Up to 3000 tessellations of points in an area of any rectangular dimensions can be scaled appropriately and viewed on computer screen or output to laser printer. 2. The program also calculates Dirichlet cell areas and their coefficient of variation (CV) as well as the average nearest neighbour distance between points. 3. Simulations revealed the polynomial relationship between the CV and the minimum spacing between points. The relationship is used to predict the percentage of maximum spacing that is exhibited by a population. This value times the maximum spacing distance possible between objects in an area (hexagonal arrangement) yields the minimum allowed distance (MAD) that is characteristic of individuals of some territorial or ‘inhibitive' species. 4. The program and relationship were used to analyse the spatial attack patterns of the bark beetles, Dendroctonus brevicomis Leconte, Tomicus piniperda (L.), and Pityogenes chalcographus (L.) and determine their MADs. All three species exhibited spacing between attack sites, in agreement with known behavioural mechanisms that are proposed for avoiding intraspecific competition for food resources.},
-author = {Byers, John A.},
-doi = {10.2307/5629},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Byers - 1992 - Dirichlet Tessellation of Bark Beetle Spatial Attack Points.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {3},
-pages = {759--768},
-title = {{Dirichlet Tessellation of Bark Beetle Spatial Attack Points}},
-url = {https://www.jstor.org/stable/5629},
-volume = {61},
-year = {1992}
-}
-@article{Bavaud2011,
-abstract = {The class of Schoenberg transformations, embedding Euclidean distances into higher dimensional Euclidean spaces, is presented, and derived from theorems on positive definite and conditionally negative definite matrices. Original results on the arc lengths, angles and curvature of the transformations are proposed, and visualized on artificial data sets by classical multidimensional scaling. A simple distance-based discriminant algorithm illustrates the theory, intimately connected to the Gaussian kernels of Machine Learning.},
-archivePrefix = {arXiv},
-arxivId = {1004.0089},
-author = {Bavaud, Fran{\c{c}}ois},
-doi = {10.1007/s00357-011-9092-x},
-eprint = {1004.0089},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bavaud - 2011 - On the Schoenberg Transformations in Data Analysis Theory and Illustrations.pdf:pdf},
-journal = {Journal of Classification},
-number = {3},
-pages = {297--314},
-title = {{On the Schoenberg Transformations in Data Analysis: Theory and Illustrations}},
-volume = {28},
-year = {2011}
-}
-@techreport{Brulhart1996,
-abstract = {This paper analyses the effects of regional integration on the location of increasing-returns industry and the resulting pattern of trade. Theoretically, it is shown that regional integration may initially lead to a dispersion of industry inside the customs union. Below a certain threshold of internal trade costs, however, industry concentration in the central member country will again increase. This non-monotonic relationship with regional integration also applies to equilibrium levels of intra-industry trade (IIT). A strictly monotonic negative relationship is found between, on one hand, the degree of scale economies and, on the other hand, industrial concentration both in the central country and intra-union IIT. Empirical evidence for the European Union lends support to some of the theoretical predictions. Employment in scale-intensive industries tends to be concentrated at the centre of the EU, and IIT is relatively low in these sectors. An IIT growth reversal is detected for the scale-intensive industries, which supports the non-monotonicity predicted by the model.},
-address = {London},
-author = {Br{\"{u}}lhart, Marius and Torstensson, Johan},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Br{\"{u}}lhart, Torstensson - 1996 - Regional Integration, Scale Economies an Industry Location in the European Union.pdf:pdf},
-publisher = {Centre for Economic Policy Research},
-title = {{Regional Integration, Scale Economies an Industry Location in the European Union}},
-url = {www.cepr.org/pubs/dps/DP1435.asp},
-year = {1996}
-}
-@article{Bolker2009,
-abstract = {How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize ‘best-practice' data analysis procedures for scientists facing this challenge.},
-author = {Bolker, Benjamin M. and Brooks, Mollie E. and Clark, Connie J. and Geange, Shane W. and Poulsen, John R. and Stevens, M Henry H. and White, Jada-Simone S.},
-doi = {10.1016/j.tree.2008.10.008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bolker et al. - 2009 - Generalized linear mixed models a practical guide for ecology and evolution.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {3},
-pages = {127--135},
-title = {{Generalized linear mixed models: a practical guide for ecology and evolution}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534709000196},
-volume = {24},
-year = {2009}
-}
-@article{Beck2013,
-abstract = {Beta diversity is a conceptual link between diversity at local and regional scales. Various additional methodologies of quantifying this and related phenomena have been applied. Among them, measures of pairwise (dis)similarity of sites are particularly popular. Undersampling, i.e. not recording all taxa present at a site, is a common situation in ecological data. Bias in many metrics related to beta diversity must be expected, but only few studies have explicitly investigated the properties of various measures under undersampling conditions. * On the basis of an empirical data set, representing near-complete local inventories of the Lepidoptera from an isolated Pacific island, as well as simulated communities with varying properties, we mimicked different levels of undersampling. We used 14 different approaches to quantify beta diversity, among them dataset-wide multiplicative partitioning (i.e. ‘true beta diversity') and pairwise site x site dissimilarities. We compared their values from incomplete samples to true results from the full data. We used these comparisons to quantify undersampling bias and we calculated correlations of the dissimilarity measures of undersampled data with complete data of sites. * Almost all tested metrics showed bias and low correlations under moderate to severe undersampling conditions (as well as deteriorating precision, i.e. large chance effects on results). Measures that used only species incidence were very sensitive to undersampling, while abundance-based metrics with high dependency on the distribution of the most common taxa were particularly robust. Simulated data showed sensitivity of results to the abundance distribution, confirming that data sets of high evenness and/or the application of metrics that are strongly affected by rare species are particularly sensitive to undersampling. * The class of beta measure to be used should depend on the research question being asked as different metrics can lead to quite different conclusions even without undersampling effects. For each class of metric, there is a trade-off between robustness to undersampling and sensitivity to rare species. In consequence, using incidence-based metrics carries a particular risk of false conclusions when undersampled data are involved. Developing bias corrections for such metrics would be desirable.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Beck, Jan and Holloway, Jeremy D and Schwanghart, Wolfgang},
-doi = {10.1111/2041-210x.12023},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beck, Holloway, Schwanghart - 2013 - Undersampling and the measurement of beta diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {4},
-pages = {370--382},
-title = {{Undersampling and the measurement of beta diversity}},
-url = {http://dx.doi.org/10.1111/2041-210x.12023},
-volume = {4},
-year = {2013}
-}
-@article{Lotwick1982,
-abstract = {Two approaches are described to the analysis of spatial patterns consisting of several types of points. The first approach uses a method of asymptotically unbiased estimation of the second moment distribution; the second uses methods based on regions of empty space in the patterns. Some distributional results are given in each case, and a method of Monte Carlo testing conditional on the marginal structure is described. The methods are illustrated by being applied to some physiological data.},
-author = {Lotwick, H. W. and Silverman, B. W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lotwick, Silverman - 1982 - Methods for Analysing Spatial Processes of Several Types of Points.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {3},
-pages = {406--413},
-title = {{Methods for Analysing Spatial Processes of Several Types of Points}},
-url = {https://www.jstor.org/stable/2345499},
-volume = {44},
-year = {1982}
-}
-@book{Haggett1977,
-address = {London},
-annote = {Traduction fran{\c{c}}aise, pp 59-61 : maillage r{\'{e}}gulier.},
-author = {Haggett, Peter and Cliff, Andrew David and Frey, Allan E},
-edition = {2nd ed},
-isbn = {0-7131-5899-9},
-pages = {1--605},
-publisher = {E. Arnold},
-title = {{Locational analysis in human geography}},
-year = {1977}
-}
-@article{Jarzyna2016,
-abstract = {Interest in, and opportunities to include functional and phylogenetic attributes of species in community ecology and biogeography are rapidly growing and seen as vital for the assessment of status and trends in biodiversity. However, the fundamental underlying evidence remains the (co-)occurrence of the biological units, such as species, in time and space and our ability to appropriately detect and quantify them. Here, we examine the implications of imperfect detection of species for functional and phylogenetic diversity (FD and PD) estimates. We explore how FD and PD might have different detectabilities than taxonomic diversity (TD) and how all three might vary differently along spatial and environmental gradients. We also extend occupancy modeling and dendrogram-based methods to address the imperfect detection of different biodiversity facets. Trait-based and phylogenetic attributes of species are increasingly seen as vital components to better address the processes underlying spatial and temporal biodiversity dynamics and the potential consequences of biodiversity change.A rapid growth in phylogenetic trees and trait compilations has led to an increase in phylogentic and functional diversity studies and resulted in numerous applications, including evaluating impacts of global change, setting conservation targets, and mapping ecosystem services.All diversity metrics remain limited by our ability to measure them in the field. The fundamental unit (the presence or abundance of a single species) is rarely perfectly captured and measurement quality varies by species, environments, and traits.The potential consequences of this imperfect detection for functional or phylogenetic diversity have to date remained unexamined.},
-author = {Jarzyna, Marta A. and Jetz, Walter},
-doi = {10.1016/j.tree.2016.04.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jarzyna, Jetz - 2016 - Detecting the Multiple Facets of Biodiversity.pdf:pdf},
-journal = {Trends in Ecology and Evolution},
-number = {7},
-pages = {527--538},
-title = {{Detecting the Multiple Facets of Biodiversity}},
-url = {http://dx.doi.org/10.1016/j.tree.2016.04.002},
-volume = {31},
-year = {2016}
-}
-@article{Sakschewski2016,
-abstract = {Climate change threatens ecosystems worldwide, yet their potential future resilience remains largely unquantified1. In recent years many studies have shown that biodiversity, and in particular functional diversity, can enhance ecosystem resilience by providing a higher response diversity. So far these insights have been mostly neglected in large-scale projections of ecosystem responses to climate change6. Here we show that plant trait diversity, as a key component of functional diversity, can have a strikingly positive effect on the Amazon forests' biomass under future climate change. Using a terrestrial biogeochemical model that simulates diverse forest communities on the basis of individual tree growth7, we show that plant trait diversity may enable the Amazon forests to adjust to new climate conditions via a process of ecological sorting, protecting the Amazon's carbon sink function. Therefore, plant trait diversity, and biodiversity in general, should be considered in large-scale ecosystem projections and be included as an integral part of climate change research and policy.},
-author = {Sakschewski, Boris and von Bloh, Werner and Boit, Alice and Poorter, Lourens and Pe{\~{n}}a-Claros, Marielos and Heinke, Jens and Joshi, Jasmin and Thonicke, Kirsten},
-doi = {10.1038/nclimate3109},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sakschewski et al. - 2016 - Resilience of Amazon forests emerges from plant trait diversity.pdf:pdf},
-journal = {Nature Climate Change},
-pages = {1032--1036},
-title = {{Resilience of Amazon forests emerges from plant trait diversity}},
-url = {http://www.nature.com/doifinder/10.1038/nclimate3109},
-volume = {6},
-year = {2016}
-}
-@article{Guan2007,
-abstract = {The K-function is a popular tool for fitting spatial point process models owing to its simplicity and wide applicability. In this work we study the properties of least squares estimators of model parameters and propose a new method of model fitting via the K-function by using subsampling. We demonstrate consistency and asymptotic normality of our estimators of model parameters and compare the efficiency of our procedure with existing procedures. This is done through asymptotic theory, simulation experiments and an application to a data set on long leaf pine-trees.},
-annote = {Guan, Yongtao Sherman, Michael
-Part 1},
-author = {Guan, Yontao and Sherman, Michael},
-doi = {10.1111/j.1467-9868.2007.00575.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan, Sherman - 2007 - On least squares fitting for stationary spatial point processes.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {31--49},
-title = {{On least squares fitting for stationary spatial point processes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9868.2007.00575.x/abstract},
-volume = {69},
-year = {2007}
-}
-@article{Cutrini2010,
-abstract = {This paper investigates European location patterns during a period of economic integration, seeking to identify the distinct roles played by the different geographical levels. The evolution of localization in Europe proved much more complicated empirically than the predictions based on Krugman's hypothesis. Using Eurostat regional data for the period 1985-2001, the paper shows that while manufacturing employment trickled down among regions, after the completion of the European Single Market a slight agglomeration occurred, but only across national boundaries. National specialization has emerged particularly in the European Union founding Member States. Moreover, there is evidence of an increasing polarization of the North-South divide closely connected with the growing concentration of high-technology sectors.},
-author = {Cutrini, Eleonora},
-doi = {10.1080/00343400802378743},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cutrini - 2010 - Specialization and Concentration from a Twofold Geographical Perspective Evidence from Europe.pdf:pdf},
-journal = {Regional Studies},
-number = {3},
-pages = {315--336},
-title = {{Specialization and Concentration from a Twofold Geographical Perspective: Evidence from Europe}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/00343400802378743},
-volume = {44},
-year = {2010}
-}
-@article{Maasoumi1993,
-abstract = {An extensive synthesis is provided of the concepts, measures and techniques of Information Theory (IT). After an axiomatic description of the basic definitions of “information functions”, “entropy” or uncertainty and the maximum entropy principle, the paper demonstrates the power of IT as both an interpretive and techinically productive tool. It is argued that this power and universality is promarily due to the common need for (i) measures of distance and discrimination and, (ii) appropriate partitioning- aggregation properties. IT offers a very suggestive unification for a bewildering and arbitrary set of approaches that have evolved in different disciplines. Applications are discussed or indicated. These applications have relevance to economics, finance, industrial organization, marketing, statistical ingerence and model selection, political science and communication. A main focus of the discussion is the generative power of IT measures in statistical examinations of unknown distributions and random phenomena. Measures of concentration and inequality, aggregation functions and index numbers, tests of nested and non{\_}nested hypotheses, and measures of volatility, movility and divergence are presented. Extending the author's previous work, estimation of unknown regression functions, densities and score functions is examined based on the maximum entropy principle. Some empirical examples are cited.},
-annote = {0747-4938},
-author = {Maasoumi, Esfandiar},
-doi = {10.1080/07474939308800260},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Maasoumi - 1993 - A compendium to information theory in economics and econometrics.pdf:pdf},
-journal = {Econometric Reviews},
-number = {2},
-pages = {137--181},
-title = {{A compendium to information theory in economics and econometrics}},
-url = {http://www.informaworld.com/10.1080/07474939308800260},
-volume = {12},
-year = {1993}
-}
-@article{Ricotta2003d,
-abstract = {A desirable property of a diversity index is strict concavity. This implies that the pooled diversity of a given community sample is greater or equal to but no less than the weighted mean of the diversity values of the consituting plots. For a strict concave diversity index, such as species richness S, Shannon's entropy H and Simpson's index 1-D, the pooled diversity of a given community sample can be partitioned into two non-negative, additive components: average within-plot diversity and between-plot diversity. As a result, species diversity can be summarized at various scales measuring all diversity components in the samen unit. Conversely, violation of strict concavity would imply the non-interpretable result of a negative diversity among community plots. In this paper, I apply this additive partition model generally adpted for traditional diversity measures to Aczel and DAroczy generalized entropy of type A. In htis way, a parametric mesaure of B-diversity is derived as the ratio between the pooled sample diversity and the average within plot diversity that represents the parametric analogue of Whittaker's B-diversity for data on species relative abundances.},
-annote = {Mauvaise approche: d{\'{e}}finit H{\_}beta comme H{\_}gamma/H{\_}alpha},
-author = {Ricotta, Carlo},
-doi = {10.1023/A:1024539526618},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2003 - Additive partition of parametric infromation and its associated $\beta$-diversity measure.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {2},
-pages = {91--100},
-title = {{Additive partition of parametric infromation and its associated $\beta$-diversity measure}},
-url = {https://link.springer.com/article/10.1023{\%}2FA{\%}3A1024539526618},
-volume = {51},
-year = {2003}
-}
-@article{Wright2004,
-abstract = {Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.},
-author = {Wright, Ian J. and Reich, Peter B. and Westoby, Mark and Ackerly, David D. and Baruch, Zdravko and Bongers, Frans and Cavender-Bares, Jeannine and Chapin, Terry and Cornelissen, Johannes H. C. and Diemer, Matthias and Flexas, Jaume and Garnier, Eric and Groom, Philip K. and Gulias, Javier and Hikosaka, Kouki and Lamont, Byron B. and Lee, Tali and Lee, William and Lusk, Christopher and Midgley, Jeremy J. and Navas, Marie-Laure and Niinemets, {\"{U}}lo and Oleksyn, Jacek and Osada, Noriyuki and Poorter, Hendrik and Poot, Pieter and Prior, Lynda and Pyankov, Vladimir I. and Roumet, Catherine and Thomas, Sean C. and Tjoelker, Mark G. and Veneklaas, Erik J. and Villar, Rafael},
-doi = {10.1038/nature02403},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2004 - The worldwide leaf economics spectrum.pdf:pdf},
-journal = {Nature},
-pages = {821--827},
-title = {{The worldwide leaf economics spectrum}},
-volume = {428},
-year = {2004}
-}
-@article{Chao2014a,
-abstract = {Hill numbers or the effective numberof species are increasingly used to quantify species diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity, which incorporates species evolutionary history, as well as to functional diversity, which considers the differences among species traits. We review these extensions and integrate them into a framework of attribute diversity (the effective number of entities or total attribute value) based on Hill numbers of taxonomic entities (species), phylogenetic entities (branches of unit-length), or functional entities (species-pairs with unit-distance between species). This framework unifies ecologists' measures of species diversity, phylogenetic diversity, and distance-based functional diversity. It also provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of the classic Jaccard, S{\o}rensen, Horn, and Morisita-Horn indexes. A real example shows how this framework extracts ecological meaning from complex data.},
-author = {Chao, Anne and Chiu, Chun-Huo and Jost, Lou},
-doi = {10.1146/annurev-ecolsys-120213-091540},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu, Jost - 2014 - Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity and Related Similarity Differentiatio.pdf:pdf},
-journal = {Annual Review of Ecology, Evolution, and Systematics},
-pages = {297--324},
-title = {{Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity and Related Similarity /Differentiation Measures Through Hill Numbers}},
-url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-120213-091540},
-volume = {45},
-year = {2014}
-}
-@article{Billings2012,
-abstract = {We construct the location quotient (LQ) from a discrete data generating process and formally test its statistical properties. First, we show that the LQ is typically unbiased, but exhibits finite sample bias when assuming a Poisson distribution. Second, we determine the accuracy of statistical tests, which depends of both sample size as well as desired confidence levels. After constructing LQs using County Business Patterns (2000) data, we find improved accuracy in statistical tests when one increases spatial as well as industrial aggregation. Results show a clear tradeoff between precise statistical inference and power in detecting industrial concentration.},
-author = {Billings, Stephen B. and Johnson, Erik B.},
-doi = {10.1016/j.regsciurbeco.2012.03.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Billings, Johnson - 2012 - The location quotient as an estimator of industrial concentration.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {4},
-pages = {642--647},
-title = {{The location quotient as an estimator of industrial concentration}},
-volume = {42},
-year = {2012}
-}
-@article{Sokol2016,
-abstract = {To understand controls over biodiversity, it is necessary to take a multi-scale approach to understand how local and regional factors affect the community assembly processes that drive emergent patterns. This need is reflected in the growing use of the metacommunity concept to interpret multi-scale measures of biodiversity, including metrics derived from diversity partitioning (e.g. $\alpha$, $\beta$ and $\gamma$ diversity) and variation partitioning (e.g. spatial and environmental components of compositional turnover) techniques. However, studies have shown limited success using these metrics to characterize underlying community assembly dynamics. Here we demonstrate how a metacommunity simulation package (MCSim) can be used to evaluate when and how biodiversity metrics can be used to make inferences about metacommunity characteristics. We examined a wide range of parameter settings representing ecologically relevant scenarios. We used artificial neural networks (ANNs) to assess the sensitivity of diversity and variation partitioning metrics (calculated from simulation outcomes) to metacommunity parameter settings. In the scenarios examined in this study, the niche-neutral gradient strongly influenced most biodiversity metrics, metacommunity size exhibited a marginal influence over some metrics, and dispersal dynamics only affected a subset of variation partitioning outcomes. Variation partitioning response curves along the niche-neutral gradient were not monotonic; however, simulation outcomes suggest other biodiversity metrics (e.g. dissimilarity saturation) can be used in combination with variation partitioning metrics to make inferences about metacommunity properties. With the growing availability of archived ecological data, we expect future work will apply simulation-based techniques to better understand links between biodiversity and the metacommunity characteristics that are presumed to control the underlying community assembly processes.},
-author = {Sokol, Eric R. and Brown, Bryan L. and Barrett, J. E.},
-doi = {10.1111/oik.03690},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sokol, Brown, Barrett - 2016 - A simulation-based approach to understand how metacommunity characteristics influence emergent biodiversi.pdf:pdf},
-journal = {Ecography},
-title = {{A simulation-based approach to understand how metacommunity characteristics influence emergent biodiversity patterns}},
-url = {http://onlinelibrary.wiley.com/wol1/doi/10.1111/oik.03690/abstract},
-volume = {in press},
-year = {2016}
-}
-@article{Gregori2016,
-abstract = {Mutant spectrum dynamics (changes in the related mutants that compose viral populations) has a decisive impact on virus behavior. The several platforms of next generation sequencing (NGS) to study viral quasispecies offer a magnifying glass to study viral quasispecies complexity. Several parameters are available to quantify the complexity of mutant spectra, but they have limitations. Here we critically evaluate the information provided by several population diversity indices, and we propose the introduction of some new ones used in ecology. In particular we make a distinction between incidence, abundance and function measures of viral quasispecies composition. We suggest a multidimensional approach (complementary information contributed by adequately chosen indices), propose some guidelines, and illustrate the use of indices with a simple example. We apply the indices to three clinical samples of hepatitis C virus that display different population heterogeneity. Areas of virus biology in which population complexity plays a role are discussed.},
-author = {Gregori, Josep and Perales, Celia and Rodriguez-Frias, Francisco and Esteban, Juan I. and Quer, Josep and Domingo, Esteban},
-doi = {10.1016/j.virol.2016.03.017},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregori et al. - 2016 - Viral quasispecies complexity measures.pdf:pdf},
-journal = {Virology},
-pages = {227--237},
-title = {{Viral quasispecies complexity measures}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S004268221630037X},
-volume = {493},
-year = {2016}
-}
-@article{Ellison1997,
-abstract = {This paper discusses the prevalence of Silicon Valley-style localizations of individual manufacturing industries in the United States. A model in which localized industry-specific spillovers, natural advantages, and pure random chance all contribute to geographic concentration is used to develop a test for whether observed levels of concentration are greater than would be expected to arise randomly and to motivate new indices of geographic concentration and of coagglomeration. The proposed indices control for differences in the size distribution of plants and for differences in the size of the geographic areas for which data are available. As a consequence, comparisons of the degree of geographic concentration across industries can be made with more confidence. Our empirical results provide a strong reaffirmation of the previous wisdom in that we find almost all industries to be somewhat localized. In many industries, however, the degree of localization is slight. We explore the nature of agglomerative forces in describing patterns of concentration, the geographic scope of localization, and the coagglomeration of related industries and of industries with strong upstream-downstream ties.},
-author = {Ellison, Glenn and Glaeser, Edward L},
-doi = {10.1086/262098},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ellison, Glaeser - 1997 - Geographic Concentration in U.S. Manufacturing Industries A Dartboard Approach.pdf:pdf},
-journal = {Journal of Political Economy},
-number = {5},
-pages = {889--927},
-title = {{Geographic Concentration in U.S. Manufacturing Industries: A Dartboard Approach}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/262098},
-volume = {105},
-year = {1997}
-}
-@article{Peet1974,
-author = {Peet, Robert K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peet - 1974 - The measurement of species diversity.pdf:pdf},
-journal = {Annual review of ecology and systematics},
-pages = {285--307},
-title = {{The measurement of species diversity}},
-url = {http://www.jstor.org/stable/2096890},
-volume = {5},
-year = {1974}
-}
-@book{Stoyan1987,
-address = {New York},
-annote = {Texte int{\'{e}}gral dans Chiu, Soyan et al.: troisi{\`{e}}me {\'{e}}dition.},
-author = {Stoyan, Dietrich and Kendall, W. S. and Mecke, Joseph},
-booktitle = {Wiley Series in probability and mathematical statistics},
-publisher = {John Wiley {\&} Sons},
-title = {{Stochastic Geometry and its Applications}},
-year = {1987}
-}
-@article{Ricotta2009a,
-abstract = {In this paper, expanding on a well-known connection between Whittaker's beta diversity and multivariate dissimilarity coefficients, a simple test for differences in beta diversity among different sets of plots is proposed. Being based on any suitable (not necessarily symmetric) plot-to-plot dissimilarity coefficient the test is appropriate for analyzing multivariate data that are usually zero-inflated due to the large number of rare species and for which the number of variables (species) is typically larger than the number of observations (plots). To illustrate the proposed test in practice, we used data from two beech forests with different management history in Abruzzo (central Italy). {\textcopyright} 2008 Elsevier Ltd. All rights reserved.},
-annote = {Cited By (since 1996):13
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo and Burrascano, Sabina},
-doi = {10.1016/j.ecolind.2008.09.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Burrascano - 2009 - Testing for differences in beta diversity with asymmetric dissimilarities.pdf:pdf},
-journal = {Ecological Indicators},
-number = {4},
-pages = {719--724},
-title = {{Testing for differences in beta diversity with asymmetric dissimilarities}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-58149475028{\&}partnerID=40{\&}md5=f5f9e30da55a5ec5d39ce279580cc0e0},
-volume = {9},
-year = {2009}
-}
-@article{Odum1950,
-author = {Odum, Eugene P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Odum - 1950 - Bird Populations of the Highlands (North Carolina) Plateau in Relation to Plant Succession and Avian Invasion.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {587--605},
-title = {{Bird Populations of the Highlands (North Carolina) Plateau in Relation to Plant Succession and Avian Invasion}},
-volume = {31},
-year = {1950}
-}
-@techreport{Amiti1997,
-author = {Amiti, Mary},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Amiti - 1999 - Specialization Patterns in Europe.pdf:pdf},
-isbn = {363},
-publisher = {Centre for Economic Performance},
-title = {{Specialisation Patterns in Europe}},
-year = {1997}
-}
-@misc{Cadotte2017,
-abstract = {Environmental filtering, where the environment selects against certain species, is thought to be a major mechanism structuring communities. However, recent criticisms cast doubt on our ability to accurately infer filtering because competition can give rise to patterns identical to those caused by environmental filtering. While experiments can distinguish mechanisms, observational patterns are especially problematic. The environment determines community composition not only directly via survival, but also by influencing competition. If species population growth rates covary with environmental gradients, then outcomes of competitive exclusion will also vary with the environment. Here, we argue that observational studies remain valuable, but inferences about the importance of the environment cannot rely on compositional data alone, and that species abundances, population growth, or traits must be correlated with the environment.},
-author = {Cadotte, Marc W. and Tucker, Caroline M.},
-booktitle = {Trends in Ecology and Evolution},
-doi = {10.1016/j.tree.2017.03.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte, Tucker - 2017 - Should Environmental Filtering be Abandoned.pdf:pdf},
-number = {6},
-pages = {429--437},
-title = {{Should Environmental Filtering be Abandoned?}},
-volume = {32},
-year = {2017}
-}
-@article{Petchey2004,
-abstract = {1. Changes in biodiversity can affect ecosystem processes through a variety of pathways, such as changes in community structure, loss of a keystone or changes in resource use patterns among species. The latter, also known as resource use complementarity, is an established mechanistic link between species and ecosystems. 2. At present, functional group richness is the dominant measure of the extent of resource use complementarity and has been manipulated in several experiments. These groups are constructed a priori using information about differences between species and a statistically significant effect is typically identified by standard parametric tests. These tests implicitly assume that the a priori functional groups are correct. 3. Avoiding this assumption requires a randomization (bootstrap) test of statistical significance that accounts for the effects of grouping per se . This test compares the observed test statistic to the distribution of the test statistic resulting from random assignment of species to groups. 4. Re-analyses of experimental manipulations of plant functional diversity by bootstrapping the critical significance value changed the ecological interpretation of results in nearly half of the experiments. This occurred because random assignment of species to functional groups frequently creates a strong relationship between functional diversity and ecosystem functioning. 5. The significant bootstrapped results that were found perhaps represent some of the most convincing evidence that functional diversity is an important determinant of local-scale ecosystem functioning.},
-annote = {Article},
-author = {Petchey, Owen L.},
-doi = {10.1111/j.0269-8463.2004.00852.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Petchey - 2004 - On the statistical significance of functional diversity effects.pdf:pdf},
-journal = {Functional Ecology},
-number = {3},
-pages = {297--303},
-title = {{On the statistical significance of functional diversity effects}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0269-8463.2004.00852.x/abstract},
-volume = {18},
-year = {2004}
-}
-@article{Usher1983,
-abstract = {(1) Grids of 1500 (300 x 5 ) 2 x 2 cm quadrats have been recorded on three moss-turf sites: South Georgia in the Sub-Antarctic (three dominant species), and in the maritime Antarctic on Signy Island (two dominant species) and on Galindez Island (a virtual monoculture of Polytrichurn alpestre). (2) Two methods of pattern analysis, the stepped blocked quadrats variance method and the two-term local quadrat variance method, have been used on all data. It is stressed that there is as yet no satisfactory technique for exploring pattern in belt transects. (3) It is suggested that the pattern in the simplest of these communities, Galindez Island, is due to the alternation of mossy areas, or hummocks, and bare ground. (4) At Signy Island there is a well developed pattern, with two scales of heterogeneity at about 20 cm and at 1.2-2.0 m. The latter is considered to be due to the history of vegetation development, which is determined by the distribution of rocks now beneath the surface of the moss carpet. (5) The South Georgia community has two scales of pattern similar to those on Signy Island, but the factors determining them are unknown. In this three-species community both positive and negative associations are indicated. (6) On all sites, virtually all analyses indicated a small scale of pattern at about 20 cm. It is considered that this scale is important when sampling both the vegetation and the animal communities living within the moss-turf communities.},
-author = {Usher, M. B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Usher - 1983 - Pattern in the Simple Moss-Turf Communities of the Sub-Antarctic ant Maritime Antarctic.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {945--958},
-title = {{Pattern in the Simple Moss-Turf Communities of the Sub-Antarctic ant Maritime Antarctic}},
-volume = {71},
-year = {1983}
-}
-@misc{Morin2001,
-author = {Morin, Antoine and Findlay, Scott},
-title = {{Biodiversit{\'{e}} : tendances et processus}},
-url = {http://simulium.bio.uottawa.ca/bio3515/pdf/presentations/02-Biodiversite.pdf},
-year = {2001}
-}
-@article{Roggy1999,
-abstract = {The natural '5N abundance method for estimating symbiotic biolo- gical N2-fixation was tested on legume trees from two rain forests on contrasting soils (oxisols and spodosols) in Frenich Guiana. When possible, the siglnificance of N2-fixing species in the plant community was evaluated in terms of density, bio- mass and contribution of N2-fixation to the building up of the total nitrogen mass in the leaves. Of the two sites, the rain forest on spodosols was the less favourable for application of the 6'5N method: the available soil nitrogen was isotopically similar to fixed-N2. Hence, the results showed that a reliable estimate of N2- fixation could not be obtained. A substantial contribution of fixed-N2 to the nitro- gen nutrition of legumes was found on oxisols, with an average value of 54 {\%} Ndfa (Nitrogen derived from the atmosphere). The contribution of the N2-fixing leg- umes to the biomass of the stand was estimated to be 2 t ha-' for the leaf biomass and 136 t ha-' for the total above-ground plant biomass. With 7.5 {\%} of trees in the stand able to fix N2 (462 out of 6156), N2-fixation was estimated to be 7 kg ha-' y-'. These results are the first use of the 6'5N method to estimate nitrogen input by N2-fixing legumes to a natural rain forest. The inter-site variability observed in the 6'5N of the non-fixing plants suggested different nitrogen-cycling processes in the two soils. The 6'5N of the non-N2-fixing plants could be related to the soil nitrogen availability and be used as an indicator of efficient or non-efficient nitro- gen-cycling rain forests. The spatial variability of the 6'"N in the plant-available soil nitrogen pool and the nitrogen balance in tropical rain forests are discussed.},
-annote = {DB 798
-AGM 78},
-author = {Roggy, Jean-Christophe and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roggy et al. - 1999 - Nitrogen cycling in the tropical rain forest of french Guiana comparison of two sites with contrasting soil types.pdf:pdf},
-journal = {New Phytologist},
-pages = {283--294},
-title = {{Nitrogen-fixing legumes and silvigenesis in a rain forest in French Guiana: a taxonomic and ecological approach}},
-volume = {144},
-year = {1999}
-}
-@article{Shimatani2004,
-abstract = {This paper developed statistical methods for quantitatively assessing spatial pattern of communities with abundant species richness such as in tropical forests. Based on multivariate point processes, species richness and the Simpson's diversity index can be extended to the functions illustrating basic characteristics of multispecies spatial pattern. The spatial extension of the species richness is a sum of the detectabilities of constituent species within a given distance. By means of calculating the functions for individuals belonging to specific size class, the size structure of multispecies spatial pattern can also be examined. Therefore, comprehensive analysis of species, size, and spatial pattern together with the roles of each species in a community can be conducted. This paper demonstrated its descriptive utility in exploratory analysis by applications to four subtropical forest tree communities of different ages in Okinawa Island, southern Japan, all of which have abundant species richness. The results quantitatively revealed the contrasts among the four stands ranging from a young secondary stand to an old-growth forest as well as changes of relative positions of species in communities depending on their ecologic properties.},
-author = {Shimatani, Kenichiro and Kubota, Yasuhiro},
-doi = {10.1111/j.1440-1703.2003.00619.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shimatani, Kubota - 2004 - Quantitative assessment of multispecies spatial pattern with high species diversity.pdf:pdf},
-journal = {Ecological Research},
-number = {2},
-pages = {149--163},
-title = {{Quantitative assessment of multispecies spatial pattern with high species diversity}},
-url = {http://dx.doi.org/10.1111/j.1440-1703.2003.00619.x},
-volume = {19},
-year = {2004}
-}
-@techreport{Marcon2003,
-author = {Marcon, Eric},
-booktitle = {mimeo},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon - 2003 - A note on Industry characteristics linked to establishment concentrations in nonmetropolitan areas confirming the validi.pdf:pdf},
-title = {{A note on "Industry characteristics linked to establishment concentrations in nonmetropolitan areas" confirming the validity of Ellison and Glaeser's index}},
-year = {2003}
-}
-@article{Cavender-Bares2004,
-abstract = {Closely related species that occur together in communities and experience similar environmental conditions are likely to share phenotypic traits because of the process of environmental filtering. At the same time, species that are too similar are unlikely to co-occur because of competitive exclusion. In an effort to explain the coexistence of 17 oak species within forest communities in North Central Florida, we examined correlations between the phylogenetic relatedness of oak species, their degree of co-occurrence within communities and niche overlap across environmental gradients, and their similarity in ecophysiological and life-history traits. We show that the oaks are phylogenetically overdispersed because co-occurring species are more distantly related than expected by chance, and oaks within the same clade show less niche overlap than expected. Hence, communities are more likely to include members of both the red oak and the white + live oak clades than only members of one clade. This pattern of phylogenetic overdispersion arises because traits important for habitat specialization show evolutionary convergence. We hypothesize further that certain conserved traits permit coexistence of distantly related congeners. These results provide an explanation for how oak diversity is maintained at the community level in North Central Florida.},
-author = {Cavender-Bares, Jeannine and Ackerly, David D. and Baum, D. A. and Bazzaz, F. A.},
-doi = {10.1086/386375},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cavender-Bares et al. - 2004 - Phylogenetic overdispersion in Floridian oak communities.pdf:pdf},
-journal = {The American naturalist},
-number = {6},
-pages = {823--43},
-title = {{Phylogenetic overdispersion in Floridian oak communities.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/15266381},
-volume = {163},
-year = {2004}
-}
-@article{Chave2004,
-abstract = {I review the mathematical and biological aspects of Hubbell's (2001) neutral theory of species abundance for ecological communities, and clarify its historical connections with closely related approaches in population genetics. A selective overview of the empirical evidence for and against this theory is provided, with a special emphasis on tropical plant communities. The neutral theory predicts many of the basic patterns of biodiversity, confirming its heuristic power. The strict assumption of equivalence that defines neutrality, equivalence among individuals, finds little empirical support in general. However, a weaker assumption holds for stable communities, the equivalence of average fitness among species. One reason for the surprising success of the neutral theory is that all the theories of species coexistence satisfying the fitness equivalence assumption, including many theories of niche differentiation, generate exactly the same patterns as the neutral theory. Hubbell's neutral theory represents an important synthesis and a much needed demonstration of the pivotal role of intraspecific variability in ecology. Further improvements should lead to an explicit linking to niche-based processes. This research programme will depend crucially on forthcoming theoretical and empirical achievements.},
-author = {Chave, J{\'{e}}r{\^{o}}me},
-doi = {10.1007/s11515-008-0008-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave - 2004 - Neutral theory and community ecology.pdf:pdf},
-journal = {Ecology Letters},
-number = {3},
-pages = {241--253},
-title = {{Neutral theory and community ecology}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs11515-008-0008-z},
-volume = {7},
-year = {2004}
-}
-@article{Camarero2000,
-abstract = {The spatial structure is described of two contrasting subalpine Pinus uncinata forest-alpine grassland ecotones located in the Central Pyrenees (Ordesa and Tesso) of Spain as a preliminary step to infer the processes that produced their spatial patterns. All trees were mapped and measured within 4200 m2 rectangular plots parallel to the maximum slope and encompassing timberline and treeline. The spatial description of the ecotones was accomplished using several methodologies. Point pattern analysis (Ripley's K) was first used to quantify the spatial pattern of trees using each stem x-y coordinates. Then, surface pattern analyses (Moran and Mantel spatial correlograms) were used to quantify the spatial pattern of tree characteristics across the ecotone (size, growth-form, estimated age). At the Ordesa site, krummholz individuals showed significant and positive spatial interaction with seedlings, and P. uncinata individuals evolved from shrubby to vertical growth-forms abruptly, producing a steep spatial gradient. At the Tesso site, regeneration was concentrated near the treeline and the spatial gradient was gradual. Both ecotones formed approx equal to 45 m long zones of influence along the slope based on different variables. Wind and snow avalanches seemed to be the main controlling factors of the spatial pattern of trees at Ordesa and Tesso, respectively. The results point out the potentially different responses of treeline populations to environmental changes according to the spatial pattern.},
-author = {Camarero, Jes{\'{u}}s Julio and Guti{\'{e}}rrez, Emilia and Fortin, Marie-Jos{\'{e}}e},
-doi = {10.1016/S0378-1127(99)00241-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Camarero, Guti{\'{e}}rrez, Fortin - 2000 - Spatial pattern of subalpine forest-alpine grassland ecotones in the Spanish Central Pyrenees.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {1--16},
-title = {{Spatial pattern of subalpine forest-alpine grassland ecotones in the Spanish Central Pyrenees}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112799002418},
-volume = {134},
-year = {2000}
-}
-@article{Braak1986,
-abstract = {A new multivariate analysis technique, developed to relate community composition to known variation in the environment, is described. The technique is an extension of correspondence analysis (reciprocal averaging), a popular ordination technique that extracts continuous axes of variation from species occurrence or abundance data. Such ordination axes are typically interpreted with the help of external knowledge and data on environmental variables; this two—step approach (ordination followed by environmental gradient identification) is termed indirect gradient analysis. In the new technique, called canonical correspondence analysis, ordination axes are chosen in the light of known environmental variables by imposing the extra restriction that the axes be linear combinations of environmental variables. In this way community variation can be directly related to environmental variation. The environmental variables may be quantitative or nominal. As many axes can be extracted as there are environmental variables. The method of detrending can be incorporated in the technique to remove arch effects. (Detrended) canonical correspondence analysis is an efficient ordination technique when species have bell—shaped response curves or surfaces with respect to environmental gradients, and is therefore more appropriate for analyzing data on community composition and environmental variables than canonical correlation analysis. The new technique leads to an ordination diagram in which points represent species and sites, and vectors represent environmental variables. Such a diagram shows the patterns of variation in community composition that can be explained best by the environmental variables and also visualizes approximately the "centers" of the species distributions along each of the environmental variables. Such diagrams effectively summarized relationships between community and environment for data sets on hunting spiders, dyke vegetation, and algae along a pollution gradient.},
-author = {ter Braak, Cajo J. F.},
-doi = {10.2307/1938672},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/ter Braak - 1986 - Canonical Correspondence Analysis A New Eigenvector Technique for Multivariate Direct Gradient Analysis.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1167--1179},
-title = {{Canonical Correspondence Analysis : A New Eigenvector Technique for Multivariate Direct Gradient Analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1938672/abstract},
-volume = {67},
-year = {1986}
-}
-@article{Diggle1985a,
-abstract = {A method for estimating the local intensity of a onedimensional point process is described. The estimator uses an adaptation of Rosenblatt‘s kernel method of non-parametric probability density estimation, with a correction for end-effects. An expression for the mean squared error is derived on the assumption that the underlying process is a stationary Cox process, and this result is used to suggest a practical method for choosing the value of the smoothing constant. The performance of the estimator is illustrated using simulated data. An application to data on the locations of joints along a coal seam is described. The extension to two-dimensional point processes is noted.},
-author = {Diggle, Peter J.},
-doi = {10.2307/2347366},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle - 1985 - A Kernel Method for Smoothing Point Process Data.pdf:pdf},
-journal = {Applied Statistics},
-number = {2},
-pages = {138--147},
-title = {{A Kernel Method for Smoothing Point Process Data}},
-url = {https://www.jstor.org/stable/2347366},
-volume = {34},
-year = {1985}
-}
-@article{He1997,
-abstract = {Spatial patterns of tree species were studied in a 50-ha tropical rain forest plot in the Pasoh forest, Malaysia. This forest is characterized by a high diversity and very high number of rare species. Out of the 745 species occurring with {\textgreater} five individuals, 80.4{\%} had an aggregated distribution, 19.5{\%} were randomly distributed and one species had a regular distribution. The spatial patterns of rare vs. common species, juvenile vs. adult trees, and coarse vs. fine scales were compared. Rare species are generally less aggregated than common ones and most of the randomly distributed species are rare. Spatial patterns shift from high clumping to looser intensity or random distribution when moving from juveniles to adults for the same species. No adult tree species display a regular pattern, however. Regular distributions were rarely found; this is probably due to intraspecific competition at a local scale. There is a negative correlation between per capita death rate and population density. This study suggests that the Pasoh forest and its high diversity are subjected to multiple controlling factors, e.g., topography, spacing effect, density- dependent processes and species rarity. The importance of any factor changes across spatial and temporal scales.},
-annote = {Agr{\'{e}}gation d{\'{e}}tect{\'{e}}e par l'indice de Clark {\&} Evans},
-author = {He, FangLiang and Legendre, Pierre and Lafrankie, James V.},
-doi = {10.2307/3237248},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/He, Legendre, Lafrankie - 1997 - Distribution patterns of tree species in a Malaysian tropical rain forest.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {1},
-pages = {105--114},
-title = {{Distribution patterns of tree species in a Malaysian tropical rain forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3237248/abstract},
-volume = {8},
-year = {1997}
-}
-@article{Zorach2003,
-abstract = {Weighted flow networks are structures that arise naturally when analyzing complex systems. The countable properties of unweighted networks are not easily generalized to weighted networks. One candidate measure of complexity is the number of roles, or specialized functions in a network. It is easy to identify the number of roles in a linear or cyclic unweighted network. There is only one logically consistent way to generalize the measures of nodes, flows, connectivity, and roles into weighted networks, and these generalizations are equivalent to indices derived from information theory and used by ecologists since the late seventies. Data from ecosystem networks suggests that ecosystems inhabit a narrow window of the parameter space defined by these measures.},
-author = {Zorach, Alexander C. and Ulanowicz, Robert E.},
-doi = {10.1002/cplx.10075},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zorach, Ulanowicz - 2003 - Quantifying the complexity of flow networks How many roles are there.pdf:pdf},
-journal = {Complexity},
-number = {3},
-pages = {68--76},
-title = {{Quantifying the complexity of flow networks: How many roles are there?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/cplx.10075/abstract},
-volume = {8},
-year = {2003}
-}
-@article{Grafen1989,
-abstract = {A new statistical method called the phylogenetic regression is proposed that applies multiple regression techniques to cross-species data. It allows continuous and categorical variables to be tested for and controlled for. The new method is valid despite the problem that phylogenetically close species tend to be similar, and is designed {\textperiodcentered}to be used when information about the phylogeny is incomplete. Information about the phylogeny of the species is assumed to be available in the form of a working phylogeny, which contains multiple nodes representing ignorance about the order of splitting of taxa. The non-independence between species is divided into that due to recognized phylogeny, that is, to phylogenetic associations represented in the working phylogeny; and that due to unrecognized phylogeny. The new method uses one linear contrast for each higher node in the working phylogeny, thus applying the 'radiation principle'. For binary phylogenies the method is similar to an existing method. A criterion is suggested in the form of a simulation test for deciding on the acceptability of proposed statistical methods for analysing cross-species data with a continuous y-variable. This criterion is applied to the phylogenetic regression and to some other methods. The phylogenetic regression passes this test; the other methods tested fail it. Arbitrary choices have to be made about the covariance structure of the error in order to implement the method. It is argued that error results from omitted but relevant variables, and the implications for those arbitrary choices are discussed. One conclusion is that the dates of splits between taxa, even supplemented by rates of neutral gene evolution, do not provide the 'true' covariance structure. A pragmatic approach is adopted. Several analytical results about the phylogenetic regression are given, without proof, in a mathematical appendix. A computer program has been written in GLIM to implement the phylogenetic regression, and readers are informed how to obtain a copy.},
-author = {Grafen, A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grafen - 1989 - The Phylogenetic Regression.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1233},
-pages = {119--157},
-title = {{The Phylogenetic Regression}},
-url = {http://www.jstor.org/stable/2396904},
-volume = {326},
-year = {1989}
-}
-@article{Mouquet2003,
-abstract = {We present a model of a source-sink competitive metacommunity, defined as a regional set of communities in which local diversity is maintained by dispersal. Although the conditions of local and regional coexistence have been well defined in such systems, no study has attempted to provide clear predictions of classical community-wide patterns. Here we provide predictions for species richness, species relative abundances, and community-level functional properties (productivity and space occupation) at the local and regional scales as functions of the proportion of dispersal between communities. Local (alpha) diversity is maximal at an intermediate level of dispersal, whereas between-community (beta) and regional (gamma) diversity decline as dispersal increases because of increased homogenization of the metacommunity. The relationships between local and regional species richness and the species rank abundance distributions are strongly affected by the level of dispersal. Local productivity and space occupation tend to decline as dispersal increases, resulting in either a hump-shaped or a positive relationship between species richness and productivity, depending on the scale considered (local or regional). These effects of dispersal are buffered by decreasing species dispersal success. Our results provide a niche-based alternative to the recent neutral-metacommunity model and have important implications for conservation biology and landscape management.},
-author = {Mouquet, Nicolas and Loreau, Michel},
-doi = {10.1086/378857},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouquet, Loreau - 2003 - Community patterns in source-sink metacommunities.pdf:pdf},
-journal = {The American naturalist},
-number = {5},
-pages = {544--57},
-title = {{Community patterns in source-sink metacommunities}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/14618534},
-volume = {162},
-year = {2003}
-}
-@article{Caldarelli2002,
-abstract = {A new mechanism leading to scale-free networks is proposed in this Letter. It is shown that, in many cases of interest, the connectivity power-law behavior is neither related to dynamical properties nor to preferential attachment. Assigning a quenched fitness value x(i) to every vertex, and drawing links among vertices with a probability depending on the fitnesses of the two involved sites, gives rise to what we call a good-get-richer mechanism, in which sites with larger fitness are more likely to become hubs (i.e., to be highly connected).},
-author = {Caldarelli, Guido and Capocci, A. and {De Los Rios}, P. and Mu{\~{n}}oz, Miguel A.},
-doi = {10.1103/PhysRevLett.89.258702},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Caldarelli et al. - 2002 - Scale-free networks from varying vertex intrinsic fitness.pdf:pdf},
-journal = {Physical Review Letters},
-number = {25},
-pages = {258702},
-title = {{Scale-free networks from varying vertex intrinsic fitness.}},
-volume = {89},
-year = {2002}
-}
-@unpublished{Scholl2013,
-author = {Scholl, Tobias and Brenner, Thomas},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scholl, Brenner - 2012 - Optimizing Distance-Based Methods for Big Data Analysis.pdf:pdf},
-institution = {Philipps University Marburg},
-series = {Working Papers on Innovation and Space},
-title = {{Optimizing Distance-Based Methods for Big Data Analysis}},
-url = {https://ideas.repec.org/p/pum/wpaper/2013-09.html},
-year = {2013}
-}
-@article{Maurel1997,
-author = {Maurel, Fran{\c{c}}oise},
-journal = {Economie et Pr{\'{e}}vision},
-number = {5},
-pages = {77--91},
-title = {{Evolutions locales de l'industrie 1982-1992 et convergence r{\'{e}}gionale, Quelques r{\'{e}}sultats empiriques sur donn{\'{e}}es fran{\c{c}}aises}},
-volume = {131},
-year = {1997}
-}
-@article{Reese2013,
-abstract = {1. Species richness, the number of species in a defined area, is the most frequently used biodiversity measure. Despite its intuitive appeal and conceptual simplicity, species richness is often difficult to quantify, even in well-surveyed areas, because of sampling limitations such as survey effort and species detection probability. Nonparametric estimators have generally performed better than other options, but no particular estimator has consistently performed best across variation in assemblage and survey parameters. 2. In order to evaluate estimator performances, we developed the program SimAssem. SimAssem can: (i) simulate assemblages and surveys with user-specified parameters, (ii) process existing species encounter history files, (iii) generate species richness estimates not available in other programs and (iv) format encounter history data for several other programs. 3. SimAssem can help elucidate relationships between assemblage and survey parameters and the performance of species richness estimators, thereby increasing our understanding of estimator sensitivity, improving estimator development and defining the bounds for appropriate application.},
-author = {Reese, Gordon C. and Wilson, Kenneth R. and Flather, Curtis H.},
-doi = {10.1111/2041-210X.12070},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reese, Wilson, Flather - 2013 - Program SimAssem Software for simulating species assemblages and estimating species richness.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {9},
-pages = {891--896},
-title = {{Program SimAssem: Software for simulating species assemblages and estimating species richness}},
-volume = {4},
-year = {2013}
-}
-@article{Legendre2002,
-abstract = {In ecological field surveys, observations are gathered at different spatial locations. The purpose may be to relate biological response variables (e.g., species abundances) to explanatory environmental variables (e.g., soil characteristics). In the absence of prior knowledge, ecologists have been taught to rely on systematic or random sampling designs. If there is prior knowledge about the spatial patterning of the explanatory variables, obtained from either previous surveys or a pilot study, can we use this information to optimize the sampling design in order to maximize our ability to detect the relationships between the response and explanatory variables? The specific questions addressed in this paper are: a) What is the effect (type I error) of spatial autocorrelation on the statistical tests commonly used by ecologists to analyse field survey data? b) Can we eliminate, or at least minimize, the effect of spatial autocorrelation by the design of the survey? Are there designs that provide greater power for surveys, at least under certain circumstances? c) Can we eliminate or control for the effect of spatial autocorrelation during the analysis? To answer the last question, we compared regular regression analysis to a modified t-test developed by Dutilleul for correlation coefficients in the presence of spatial autocorrelation. Replicated surfaces (typically, 1000 of them) were simulated using different spatial parameters, and these surfaces were subjected to different sampling designs and methods of statistical analysis. The simulated surfaces may represent, for example, vegetation response to underlying environmental variation. This allowed us 1) to measure the frequency of type I error (the failure to reject the null hypothesis when in fact there is no effect of the environment on the response variable) and 2) to estimate the power of the different combinations of sampling designs and methods of statistical analysis (power is measured by the rate of rejection of the null hypothesis when an effect of the environment on the response variable has been created). Our results indicate that: 1) Spatial autocorrelation in both the response and environmental variables affects the classical tests of significance of correlation or regression coefficients. Spatial autocorrelation in only one of the two variables does not affect the test of significance. 2) A broad-scale spatial structure present in data has the same effect on the tests as spatial autocorrelation. When such a structure is present in one of the variables and autocorrelation is found in the other, or in both, the tests of significance have inflated rates of type I error. 3) Dutilleul's modified t-test for the correlation coefficient, corrected for spatial autocorrelation, effectively corrects for spatial autocorrelation in the data. It also effectively corrects for the presence of deterministic structures, with or without spatial autocorrelation. The presence of a broad-scale deterministic structure may, in some cases, reduce the power of the modified t-test.},
-author = {Legendre, Pierre and Dale, Mark R T and Fortin, Marie-Jos{\'{e}}e and Gurevitch, Jessica and Hohn, Michael and Myers, Donald},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre et al. - 2002 - The Consequences of Spatial Structure for the Design and Analysis of Ecological Field Surveys.pdf:pdf},
-isbn = {09067590},
-journal = {Ecography},
-number = {5},
-pages = {601--615},
-title = {{The Consequences of Spatial Structure for the Design and Analysis of Ecological Field Surveys}},
-url = {http://www.jstor.org/stable/3683663},
-volume = {25},
-year = {2002}
-}
-@article{Szava-Kovats2014,
-abstract = {Ecologists have developed an abundance of conceptions and mathematical expressions to define $\beta$-diversity, the link between local ($\alpha$) and regional-scale ($\gamma$) richness, in order to characterize patterns of biodiversity along ecological (i.e., spatial and environmental) gradients. These patterns are often realized by regression of $\beta$-diversity indices against one or more ecological gradients. This practice, however, is subject to two shortcomings that can undermine the validity of the biodiversity patterns. First, many $\beta$-diversity indices are constrained to range between fixed lower and upper limits. As such, regression analysis of $\beta$-diversity indices against ecological gradients can result in regression curves that extend beyond these mathematical constraints, thus creating an interpretational dilemma. Second, despite being a function of the same measured $\alpha$- and $\gamma$-diversity, the resultant biodiversity pattern depends on the choice of $\beta$-diversity index. We propose a simple logistic transformation that rids beta-diversity indices of their mathematical constraints, thus eliminating the possibility of an uninterpretable regression curve. Moreover, this transformation results in identical biodiversity patterns for three commonly used classical beta-diversity indices. As a result, this transformation eliminates the difficulties of both shortcomings, while allowing the researcher to use whichever beta-diversity index deemed most appropriate. We believe this method can help unify the study of biodiversity patterns along ecological gradients.},
-author = {Szava-Kovats, Robert C. and P{\"{a}}rtel, Meelis},
-doi = {10.1371/journal.pone.0110485},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Szava-Kovats, P{\"{a}}rtel - 2014 - Biodiversity Patterns along Ecological Gradients Unifying $\beta$-Diversity Indices.pdf:pdf},
-journal = {PloS one},
-number = {10},
-pages = {e110485},
-title = {{Biodiversity Patterns along Ecological Gradients: Unifying $\beta$-Diversity Indices.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/25330181},
-volume = {9},
-year = {2014}
-}
-@article{Grabarnik2011,
-abstract = {Spatial pattern analysis provides valuable information on ecological processes. Many ecological systems can be described by marked point processes. One of the key issues in the statistical application of marked point processes is the question of spatial correlations of the marks. Therefore, the first step of analysis is a test of independence of marks.Manyresearchers use for this purpose the popular envelope test. However, this may lead to unreasonably high type I error probabilities, because in this test spatial correlations are inspected for a range of distances simultaneously. The paper discusses in detail the use of deviation tests for testing hypotheses of mark independence. Additionally, it demonstrateshowthe envelope test can be refined so that it becomes a valuable tool both for statistical inference and for understanding the reasons of possible rejections of the independence hypothesis. Two examples from forest ecology illustrate the application of both test types.},
-author = {Grabarnik, Pavel and Myllym{\"{a}}ki, Mari and Stoyan, Dietrich},
-doi = {10.1016/j.ecolmodel.2011.10.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grabarnik, Myllym{\"{a}}ki, Stoyan - 2011 - Correct testing of mark independence for marked point patterns.pdf:pdf},
-journal = {Ecological Modelling},
-number = {23-24},
-pages = {3888--3894},
-title = {{Correct testing of mark independence for marked point patterns}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S030438001100490X},
-volume = {222},
-year = {2011}
-}
-@article{Yamada2003,
-abstract = {This paper explores various edge correction, methods for K-function analysis via Monte Carlo simulation. The correction methods discussed here are Ripley's circumference correction, a toroidal correction, and a guard area correction. First, simulation envelopes for a random point pattern are constructed for each edge correction method. Then statistical powers of these envelopes are analyzed in terms of the probability of detecting clustering and regularity in simulated clustering/regularity patterns. In addition to the K-function, K(h), determined for individual distances, h, an overall statistic k is also examined. A major finding of this paper is that the K-Junction method adjusted by either the Ripley or toroidal edge correction method is more powerful than what is not adjusted or adjusted by the guard area method. Another is that the overall statistic k outperforms the individual K(h) across almost the entire range of potential distances h.},
-annote = {Article
-English
-GEOGR ANAL
-659RM},
-author = {Yamada, Ikuho and Rogerson, P A},
-doi = {10.1007/978-4-431-65958-7_20},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yamada, Rogerson - 2003 - An empirical comparison of edge effect correction methods applied to K-function analysis.pdf:pdf},
-journal = {Geographical Analysis},
-number = {2},
-pages = {97--109},
-title = {{An empirical comparison of edge effect correction methods applied to K-function analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.2003.tb01103.x/abstract},
-volume = {35},
-year = {2003}
-}
-@article{Rahbek2005,
-abstract = {Despite two centuries of exploration, our understanding of factors determining the distribution of life on Earth is in many ways still in its infancy. Much of the disagreement about governing processes of variation in species richness may be the result of differences in our perception of species-richness patterns. Until recently, most studies of large-scale species-richness patterns assumed implicitly that patterns and mechanisms were scale invariant. Illustrated with examples and a quantitative analysis of published data on altitudinal gradients of species richness (n ¼ 204), this review discusses how scale effects (extent and grain size) can influence our perception of patterns and processes. For example, a hump-shaped altitudinal species-richness pattern is the most typical (c. 50{\%}), with a monotonic decreasing pattern (c. 25{\%}) also frequently reported, but the relative distribution of patterns changes readily with spatial grain and extent. If we are to attribute relative impact to various factors influencing species richness and distribution and to decide at which point along a spatial and temporal continuum they act, we should not ask only how results vary as a function of scale but also search for consistent patterns in these scale effects. The review concludes with suggestions of potential routes for future analytical exploration of species-richness patterns.},
-author = {Rahbek, Carsten},
-doi = {10.1111/j.1461-0248.2004.00701.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rahbek - 2005 - The role of spatial scale and the perception of large-scale species-richness patterns.pdf:pdf},
-isbn = {1461-023X},
-journal = {Ecology Letters},
-number = {2},
-pages = {224--239},
-title = {{The role of spatial scale and the perception of large-scale species-richness patterns}},
-volume = {8},
-year = {2005}
-}
-@article{Levins1966,
-author = {Levins, Richard},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Levins - 1966 - The Strategy of Model Building in Population Biology.pdf:pdf},
-journal = {American Scientist},
-number = {4},
-pages = {421--431},
-title = {{The Strategy of Model Building in Population Biology}},
-url = {https://www.jstor.org/stable/27836590},
-volume = {54},
-year = {1966}
-}
-@article{Kuuluvainen1998,
-abstract = {The tree species composition, vertical stratification and patterns of spatial autocorrelation at the tree and quadrate (25 × 25 m) scales were studied in a natural mature PinuS sylvestris dominated forest in eastern Finland. For the analyses we mapped the locations and dimensions of trees taller than 10 m in a 9 ha (300 × 300 m) area, and within this area we mapped all trees taller than 0.3 m on a core plot of 4 ha (200 × 200 m). The overall tree size distribution was bimodal. the dominant layer and the understory forming the peak frequencies. Pinus sylvestris dominated the main canopy, together with scattered Betula pendula and Picea abies. Alnus incana, Populus tremula, Salix caprea, Sorbus aucuparia and Juniperus communis occurred only in the under- and middlestories. Autocorrelation analysis (semivarianee) of tree size variation revealed spatial patterns, which were strongly dependent on the size of trees included in the analysis. When all living trees, including the understory regeneration, were taken into account, the autocorrelation pattern ranged up to 35 m inter-tree distances, reflecting the spatial scale of understory regeneration patches. Competitive interaction among middle- and upperstory trees (height{\textgreater}10 m) had contrasting effects on autocorrelation pattern depending on spatial scale. At the fine scale, dominant trees suppressed their smaller close neighbors (asymmetric competition), which was shown as increased tree size variation at small inter-tree distances ({\textless}2 m). At slightly larger inter-tree distances, specifically among large trees of similar size, competition was more symmetrical, which resulted in decreased tree size variation at these inter-tree distances (3–4 m). This effect was seen most clearly in the dominant trees, there being a clear autocorrelation pattern in tree size up to inter-tree distances of ∼4 m. At the quadrate scale (25 × 25 m) the analysis revealed high local variation in structural characteristics such as tree height diversity (THD), tree species diversity (H) and autocorrelation of tree height. The analysis suggests that naturally developed P. sylvestris forests exhibit complex small-scale patterns of structural heterogeneity and spatial autocorrelation in tree size. These patterns may be important for stand-scale habitat diversity and can have aggregated effects on ecosystem dynamics at larger spatial scales though their influence on the spread of disturbance and regeneration after disturbance.},
-author = {Kuuluvainen, Timo and J{\"{a}}rvinen, E and Hokkanen, T J and Rouvinen, Seppo and Heikkinen, K},
-doi = {10.1111/j.1600-0587.1998.tb00670.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kuuluvainen et al. - 1998 - Structural heterogeneity and spatial autocorrelation in a natural mature Pinus silvestris dominated forest.pdf:pdf},
-journal = {Ecography},
-number = {2},
-pages = {159--174},
-title = {{Structural heterogeneity and spatial autocorrelation in a natural mature Pinus silvestris dominated forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.1998.tb00670.x/abstract},
-volume = {21},
-year = {1998}
-}
-@article{McGuinness1984,
-abstract = {1. The species-area curve has been studied now for more than one hundred years. In this time four hypotheses have been proposed to account for this pattern - the Random Placement (or Passive Sampling) Hypothesis, the Habitat Diversity Hypothesis, the Equilibrium Theory (or Area Per Se Hypothesis), and the Disturbance Hypothesis. The Random Placement Hypothesis was the first of these and is the simplest, proposing that nothing other than a random placement of species and individuals over area is occurring. This should be considered the Null Hypothesis for species-area studies and must be tested and rejected before any other hypothesis can be considered viable. 2. The Habitat Diversity Hypothesis explains the species-area curve via the addition of new habitats with increasing area. It is supposed to result in a Power Function curve. It has been invoked a number of times but has not yet been shown experimentally to give rise to a species-area curve. 3. The Equilibrium Theory proposes that species become extinct faster on small islands as a result of the lower population sizes on such islands. This is probably the hypothesis most frequently invoked to account for the species–area curve. It is also said to result in a species-area curve of the Power Function form. Many of the tests of this hypothesis have, however, been inadequate and on only two occasions has the null hypothesis been tested. 4. The Disturbance Hypothesis also proposes that species become extinct faster on small islands, but in this case it is supposed to occur because disturbances are more frequent and more intense on these islands. This hypothesis has only rarely been considered yet it is consistent with many of the observations used to support the Equilibrium Theory. Furthermore, it has been shown experimentally, in one situation at least, to give rise to a species-area curve. 5. Two methods exist by which the null hypothesis of Random Placement can be tested. One is based on probability calculations; the other on sampling in the field. Both methods have been successfully used to test the null hypothesis, and to demonstrate biologically interesting and meaningful patterns. 6. The existence of a Power Function curve has been taken to indicate that the Equilibrium Theory is correct. Likewise, an Exponential curve has been taken by some as indicating that Random Placement is occurring. These views can be shown, theoretically and empirically, to be invalid. The fitting of a particular type of curve does not test any of the hypotheses described. 7. Species-area curves can be meaningfully used to measure the relative species diversity of a community, and biologically interesting patterns can be found by comparing communities in this way. 8. More intensive studies, testing the null hypothesis and performing manipulative experiments, are necessary if the processes underlying the species–area curve are to be understood.},
-author = {McGuinness, Keith A.},
-doi = {10.1111/j.1469-185X.1984.tb00711.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McGuinness - 1984 - Species-area curves.pdf:pdf},
-journal = {Biological Reviews},
-number = {3},
-pages = {423--440},
-title = {{Equations and Explanations in the Study of Species-Area Curves}},
-url = {http://doi.wiley.com/10.1111/j.1469-185X.1984.tb00711.x},
-volume = {59},
-year = {1984}
-}
-@article{Thomas2002,
-abstract = {Ontogenetic changes in gas exchange parameters provide both insight into mechanisms underlying tree growth patterns, and data necessary to scale environmental impacts on young trees to predict responses of older trees. We present a quantitative review and meta-analysis of field measurements of gas exchange parameters in saplings and mature trees of 35 tree species (seven conifers, seven temperate deciduous trees, and 21 tropical evergreen trees). Data for saplings were obtained in both understory environments and open areas or large gaps. We also present data on ontogenetic changes in photosynthesis for Pseudotsuga menziesii (Mirb.) Franco and Tsuga heterophylla (Raf.) Sarg., species of particular interest because of their large maximal heights and long life-spans. Among tree species, there is evidence for both ontogenetic increases and ontogenetic decreases in photosynthetic capacity on a leaf area basis (A(area)). Overall, A(area) is generally higher for upper-canopy leaves of adult trees than for saplings, especially in temperate deciduous trees. However, the pattern for photosynthetic capacity on a leaf mass basis (A(mass)) is the reverse of that observed for A(area). Saplings of both conifers and broad-leaved trees, even when acclimated to low-light conditions, characteristically have a higher A(mass) than adult trees. This pattern is driven largely by an ontogenetic increase in leaf mass per unit area (LMA), as found in 100{\%} of studies reviewed. Data for Pacific Northwest conifers, although including measurements on some of the tallest trees studied, did not differ greatly from patterns found in other tree species. We conclude that ontogenetic changes in LMA are the single most consistent difference between saplings and adult trees, and that changes in LMA and related aspects of leaf morphology may be critical to understanding both variation in gas exchange during tree growth, and stage-dependent responses of trees to environmental change.},
-author = {Thomas, Sean C. and Winner, William E.},
-doi = {10.1093/treephys/22.2-3.117},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thomas, Winner - 2002 - Photosynthetic differences between saplings and adult trees an integration of field results by meta-analysis.pdf:pdf},
-journal = {Tree Physiology},
-number = {2-3},
-pages = {117--127},
-title = {{Photosynthetic differences between saplings and adult trees: an integration of field results by meta-analysis}},
-url = {https://doi.org/10.1093/treephys/22.2-3.117},
-volume = {22},
-year = {2002}
-}
-@article{Chao2014c,
-abstract = {Based on a sample of individuals, we focus on inferring the vector of species relative abundance of an entire assemblage and propose a novel estimator of the complete species-rank abundance distribution (RAD). Nearly all previous estimators of the RAD use the conventional ‘‘plug-in'' estimator ˆ pi (sample relative abundance) of the true relative abundance pi of species i. Because most biodiversity samples are incomplete, the plug-in estimators are applied only to the subset of species that are detected in the sample. Using the concept of sample coverage and its generalization, we propose a new statistical framework to estimate the complete RAD by separately adjusting the sample relative abundances for the set of species detected in the sample and estimating the relative abundances for the set of species undetected in the sample but inferred to be present in the assemblage. We first show that ˆ pi is a positively biased estimator of pi for species detected in the sample, and that the degree of bias increases with increasing relative rarity of each species. We next derive a method to adjust the sample relative abundance to reduce the positive bias inherent in ˆ pi. The adjustment method provides a nonparametric resolution to the longstanding challenge of characterizing the relationship between the true relative abundance in the entire assemblage and the observed relative abundance in a sample. Finally, we propose a method to estimate the true relative abundances of the undetected species based on a lower bound of the number of undetected species. We then combine the adjusted RAD for the detected species and the estimated RAD for the undetected species to obtain the complete RAD estimator. Simulation results show that the proposed RAD curve can unveil the true RAD and is more accurate than the empirical RAD. We also extend our method to incidence data. Our formulas and estimators are illustrated using empirical data sets from surveys of forest spiders (for abundance data) and soil ciliates (for incidence data). The proposed RAD estimator is also applicable to estimating various diversity measures and should be widely useful to analyses of biodiversity and community structure.},
-author = {Chao, Anne and Hsieh, T. C. and Chazdon, Robin L. and Colwell, Robert K. and Gotelli, Nicholas J.},
-doi = {10.1890/14-0550.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2015 - Unveiling the Species-Rank Abundance Distribution by Generalizing Good-Turing Sample Coverage Theory.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1189--1201},
-title = {{Unveiling the Species-Rank Abundance Distribution by Generalizing Good-Turing Sample Coverage Theory}},
-volume = {96},
-year = {2015}
-}
-@article{Ward1996,
-abstract = {In 1926, 1976, and 1986 stems (more than or equal to 10 cm diameter at 1.37 m (dbh)) were measured and mapped in a 4 ha interior study area on the Davis-Purdue Research Forest in east-central Indiana. Individual bur oak (Quercus macrocarpa) trees were aged over 300 yr old; other species were mainly oaks and Fraxinus americana. Spatial pattern type was determined using the Clark and Evans's index, and Ripley's L function. The G function was used to examine spatial dispersion at intertree distances ({\textless}20 m). Spatial pattern of combined size classes shifted from weakly non-random in 1926 to uniform in 1976 and 1986. Neighbourhood density was depressed for 2 m in 1976 and 5 m in 1986. Peak in neighbourhood density at 6 m suggested trees were spaced 6 m apart. Subcanopy (10-25 cm dbh) tree spatial pattern shifted from aggregated in 1926 to uniform in 1976. The spatial pattern of canopy ({\textgreater}25 cm dbh) trees was uniform between 1926 and 1986. Density-dependent mortality and ingrowth processes are maintaining uniform spatial distributions. Initial neighbourhood tree distribution was higher around trees which died in the periods 1926-1976 and 1976-1986 than for contemporary survivors, i.e. trees which survived this period had fewer neighbouring trees within 6 m at the beginning of the period than did trees which died. The higher initial neighbourhood densities around mortality trees than survivors supports density-dependent mortality. Ingrowth was inhibited in a 6 m zone proximate to established trees for both the 1926- 1976 and 1976-1986 periods.},
-author = {Ward, Jeffrey S. and Parker, George R. and Ferrandino, Francis J.},
-doi = {10.1016/0378-1127(96)03722-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ward, Parker, Ferrandino - 1996 - Long-term spatial dynamics in an old-growth deciduous forest.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {3},
-pages = {189--202},
-title = {{Long-term spatial dynamics in an old-growth deciduous forest}},
-url = {http://www.sciencedirect.com/science/article/pii/037811279603722X},
-volume = {83},
-year = {1996}
-}
-@article{Gotelli2010,
-abstract = {Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.},
-author = {Gotelli, Nicholas J. and Dorazio, Robert M. and Ellison, Aaron M. and Grossman, Gary D.},
-doi = {10.1098/rstb.2010.0262},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gotelli et al. - 2010 - Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1558},
-pages = {3621--3631},
-title = {{Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models.}},
-volume = {365},
-year = {2010}
-}
-@article{Guimaraes2000,
-abstract = {In urban economics, and more recently in the international economics literature, agglomeration has been offered as a principal determinant of new investment. Yet agglomeration has rarely been subject to precise statistical tests. In this paper, the availability of detailed urban and regional data for Portugal allowed for a close study of the spatial choices for newly created foreign-owned plants. It appears that agglomeration economies are decisive location factors. Service agglomeration has a notably strong effect, while industry-level localization economies and urbanization externalities are verifiable location determinants as well. Distance from the principal cities is statistically significant, but there is no evidence that local labor costs matter.},
-author = {Guimar{\~{a}}es, Paulo and Figueiredo, Oct{\'{a}}vio and Woodward, Douglas P.},
-doi = {10.1006/juec.1999.2138},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guimar{\~{a}}es, Figueiredo, Woodward - 2000 - Agglomeration and the Location of Foreign Direct Investment in Portugal.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {1},
-pages = {115--135},
-title = {{Agglomeration and the Location of Foreign Direct Investment in Portugal}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119099921381},
-volume = {47},
-year = {2000}
-}
-@article{Imbert1998,
-abstract = {In this work, we consider the role played by hurricanes in the maintenance of high biodiversity, and we look at how biodiversity may influence the response of tropical forest ecosystems to hurricane disturbances. After hurricane Hugo struck Guadeloupe in 1989, we started a comparative study on the resistance and the resilience of the rain forest, the semi-deciduous forest and the mangrove forest. It appeared that the resistance of these forests was positively linked to their diversity, which was assessed both through flora richness and structure complexity (resulting from the variety of life forms). Examples of species specific resistance or vulnerability occur in the three forests; however, the higher the ecosystem's diversity, the fewer and the weaker they are. Abundant species tend to be less vulnerable than others - at least in the rain forest and in the semi-deciduous forest. Forest recovery operates mainly through pre-existing individuals (surviving trees, coppicing stumps, saplings or seedlings). Pioneer species may slightly and temporarily benefit from large openings, especially in the rain forest. Strong recurrence of hurricanes may lead to the extinction of some rare, vulnerable, short-range disseminating, non pioneer species. (C) Elsevier, Paris.},
-author = {Imbert, Daniel and Rousteau, Alain and Labbe, Patrick},
-doi = {10.1016/S1146-609X(98)80029-5},
-journal = {Acta Oecologica-International Journal of Ecology},
-number = {3},
-pages = {251--262},
-title = {{Hurricanes and biological diversity in tropical forests - The case of Guadeloupe}},
-volume = {19},
-year = {1998}
-}
-@article{Marcon1999,
-abstract = {Cet article pr{\'{e}}sente une m{\'{e}}thode d'expertiseforesti{\`{e}}re appel{\'{e}}e “expertise arbrepar arbre”. La m{\'{e}}thode consiste {\`{a}}cal- culer la valeur d'unpeuplement forestier {\`{a}} partir d'uninventaire. La valeur d'avenir de chaque arbreest {\'{e}}valu{\'{e}}e {\`{a}} partir de sa valeur v{\'{e}}nale et d'un coefficient issu de mod{\`{e}}les. D'autre part, une v{\'{e}}rification de lacoh{\'{e}}renceentrelepeuplement r{\'{e}}el et les mod{\`{e}}les est assur{\'{e}}e. Apr{\`{e}}s quelques rappels d'{\'{e}}conomie, la m{\'{e}}thode est pr{\'{e}}sent{\'{e}}e,compar{\'{e}}e aux m{\'{e}}thodes classiques et enfin discut{\'{e}}e.},
-author = {Marcon, Eric},
-doi = {10.4267/2042/5418},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon - 1999 - Forest surveys on a tree by tree basis A theoretical and practical approach.pdf:pdf},
-journal = {Revue Foresti{\`{e}}re Fran{\c{c}}aise},
-number = {1},
-pages = {57--69},
-title = {{Forest surveys on a tree by tree basis: A theoretical and practical approach}},
-url = {http://documents.irevues.inist.fr/handle/2042/5418},
-volume = {51},
-year = {1999}
-}
-@misc{Baddeley2011,
-author = {Baddeley, Adrian J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley - 2011 - Analysing spatial point patterns in 'R'.pdf:pdf},
-publisher = {CSIRO},
-title = {{Analysing spatial point patterns in 'R'}},
-url = {http://www.csiro.au/resources/pf16h},
-year = {2011}
-}
-@article{Gadagkar1989,
-abstract = {A desirable property of a diversity index is that it be a convex function of the proportions of different species that constitute a community. N2, a diversity index belonging to the Hill's series of diversity indices and which is equivalent to the reciprocal of Simpson's diversity index violates this requirement when the proportion of one of the species is close to 1. Recommendations of N2 as the best possible index of diversity therefore need to be examined judiciously.},
-author = {Gadagkar, Raghavendra},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gadagkar - 1989 - An undesirable property of Hill's diversity index N2.pdf:pdf},
-journal = {Oecologia},
-pages = {140--141},
-title = {{An undesirable property of Hill's diversity index N2}},
-volume = {80},
-year = {1989}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2000,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret no 2000-815 du 25 ao{\^{u}}t 2000 relatif {\`{a}} l'am{\'{e}}nagement et {\`{a}} la r{\'{e}}duction du temps de travail dans la fonction publique de l'{\'{E}}tat}},
-url = {http://www.dsi.cnrs.fr/bo/2000/10-00/5216-bo1000-d2000-815du25-08-2000.htm},
-year = {2000}
-}
-@article{Hubbell2015,
-abstract = {How many tropical tree species are there in the world? Slik et al. address this question in an elegant way, but this question is far harder than one might initially suppose. Significant uncertainties still remain, which I attribute in large part to an unsolved conundrum that I call “Fisher's paradox.” Except for a few charismatic groups of organisms such as birds and butterflies, ecologists still do not know the numbers of species in most taxonomically or functionally defined groups, including tropical trees. Surveying herbaria and published species descriptions cannot tell us how many tropical tree species remain undiscovered and undescribed. Experienced tropical botanists and plant biogeographers may provide expert opinions on how many tropical tree species there are, but Slik et al. note that it is difficult to assess the accuracy of such opinions. Is there some way to come up with a more reliable estimate?},
-author = {Hubbell, Stephen P},
-doi = {10.1073/pnas.1507730112},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hubbell - 2015 - Estimating the global number of tropical tree species, and Fisher's paradox.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences},
-number = {24},
-pages = {7343--7344},
-title = {{Estimating the global number of tropical tree species, and Fisher's paradox}},
-url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1507730112},
-volume = {112},
-year = {2015}
-}
-@article{Plotkin2002,
-abstract = {The abundances and spatial distribution of species is central to biogeography and conservation. Several theories have been offered to explain landscape-scale species distribution patterns. The verification of biogeographic theories, as well as conservation decisions, must be based upon empirical data gathered from necessarily restricted censuses. It is necessary, therefore, to understand the relationship between an underlying landscape- scale pattern and the corresponding pattern it produces upon sampling small subregions. The similarity of species composition between two samples depends not only on the species composition of the underlying landscape from which the samples are drawn, but also on the underlying distribution of species abundances, the degree of conspecific spatial clus- tering, and sample size. In this paper, we investigate how sampling expectations change depending upon species abundance distributions and upon spatial distributions. We derive analytical results for the expected species overlap between two sampled regions under a wide range of conditions. We compare these results with data from a 50-ha tropical forest census. These methodologies provide useful tools for assessing beta diversity, for testing macro-ecological theory, and for designing landscape-scale sampling schemes. Key},
-author = {Plotkin, Joshua B. and Muller-Landau, Helene C.},
-doi = {10.1890/0012-9658(2002)083[3344:STSCOA]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Plotkin, Muller-Landau - 2002 - Sampling the species composition of a landscape.pdf:pdf},
-journal = {Ecology},
-number = {12},
-pages = {3344--3356},
-title = {{Sampling the species composition of a landscape}},
-url = {http://www.esajournals.org/doi/full/10.1890/0012-9658(2002)083{\%}255B3344:STSCOA{\%}255D2.0.CO;2},
-volume = {83},
-year = {2002}
-}
-@article{DeBello2013,
-abstract = {Question: Many functional diversity indices require the calculation of functional trait dissimilarities between species. However, very little is known about how the dissimilarity measure used might affect conclusions about ecological processes drawn from functional diversity. Methods: We simulated real applications of functional diversity, to illustrate the key properties of the two most common families of dissimilarity measures: (1) Gower' distance, using only mean trait' value per species and then standardizing each trait, e.g. relative to its range; (2) trait overlap' between species, which takes into account within-species trait variability. We then examine how these approaches could affect conclusions about ecological processes commonly assessed with functional diversity. We also propose a new R function (trova', i.e. TRait OVerlAp) which performs computations to estimate species trait dissimilarity with different types of data. Results: The trait overlap approach generally produces a less context-dependentmeasure of functional dissimilarity. For example, the results are less dependent on the transformation of trait data (often required in empirical datasets) and on the particular pool of species considered (i. e. trait range, regularity and presence of outliers). The results therefore could bemore easily compared across studies and biomes. Further, trait overlap more reliably reproduces patterns expected when niche differentiation structures communities. The Gower approach, on the contrary, more reliably detects environmental filtering effects. Conclusion: The two approaches imply different conceptions of how species dissimilarities relate to niche differentiation. Trait overlap is suitable for testing the effect of species interactions on functional diversity within local communities, especiallywhen relatively small differences in species traits are linked to different resource acquisition. Gower is better suited to detecting changes in functional diversity along environmental gradients, as greater differences in trait values reflect increased niche differentiation. Combining trait overlap and Gower approachesmay provide a novel way to assess the joint effects of environmental filtering and niche complementarity on community assembly. We suggest that attention should be given not only to the index of functional diversity considered but also whether the dissimilarity used is appropriate for the study context.},
-author = {{De Bello}, Francesco and Carmona, Carlos P. and Mason, Norman W. H. and Sebasti{\`{a}}, Maria Teresa and Lep{\v{s}}, Jan},
-doi = {10.1111/jvs.12008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/De Bello et al. - 2013 - Which trait dissimilarity for functional diversity Trait means or trait overlap(2).pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-title = {{Which trait dissimilarity for functional diversity: Trait means or trait overlap?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/jvs.12008/abstract},
-volume = {24},
-year = {2013}
-}
-@article{Coste2005,
-abstract = {Variability of leaf traits related to photosynthesis was assessed in seedlings from 14 tree species growing in the tropical rain forest of French Guiana. Leaf photosynthetic capacity (maximum rate of carboxylation and maximum rate of electron transport) was estimated by fitting a biochemical model of photosynthesis to response curves of net CO2 assimilation rate versus intercellular CO2 mole fraction. Leaf morphology described by leaf mass per unit leaf area (LMA), density and thickness, as well as area- and mass-based nitrogen (N) and carbon (C) concentrations, were recorded on the same leaves. Large interspecific variability was detected in photosynthetic capacity as well as in leaf structure and leaf N and C concentrations. No correlation was found between leaf thickness and density. The correlations between area- and mass-based leaf N concentration and photosynthetic capacity were poor. Conversely, the species differed greatly in relative N allocation to carboxylation and bioenergetics. Principal component analysis (PCA) revealed that, of the recorded traits, only the computed fraction of total leaf N invested in photosynthesis was tightly correlated to photosynthetic capacity. We also used PCA to test to what extent species with similar shade tolerances displayed converging leaf traits related to photosynthesis. No clear-cut ranking could be detected among the shade-tolerant groups, as confirmed by a one-way ANOVA. We conclude that the large interspecific diversity in photosynthetic capacity was mostly explained by differences in the relative allocation of N to photosynthesis and not by leaf N concentration, and that leaf traits related to photosynthetic capacity did not discriminate shade-tolerance ranking of these tropical tree species. PMID: 15996956},
-author = {Coste, Sabrina and Roggy, Jean-Christophe and Imbert, Pascal and Born, C{\'{e}}line and Bonal, Damien and Dreyer, Erwin},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coste et al. - 2005 - Leaf photosynthetic traits of 14 tropical rain forest species in relation to leaf nitrogen concentration and shade.pdf:pdf},
-journal = {Tree Physiology},
-number = {9},
-pages = {1127--1137},
-title = {{Leaf photosynthetic traits of 14 tropical rain forest species in relation to leaf nitrogen concentration and shade tolerance}},
-url = {https://www.ncbi.nlm.nih.gov/pubmed/15996956},
-volume = {25},
-year = {2005}
-}
-@techreport{Hallet2000,
-address = {Brussels},
-author = {Hallet, Martin},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hallet - 2000 - Regional Specialisation and Concentration in the EU.pdf:pdf},
-keywords = {Hallet (2000).pdf},
-mendeley-tags = {Hallet (2000).pdf},
-publisher = {European Commission},
-title = {{Regional Specialisation and Concentration in the EU}},
-year = {2000}
-}
-@article{Savage2006,
-abstract = {Nee et al. (Reports, 19 August 2005, p. 1236) used a null model to argue that life history invariants are illusions. We show that their results are largely inconsequential for life history theory because the authors confound two definitions of invariance, and rigorous analysis of their null model demonstrates that it does not match observed data.},
-author = {Savage, Van M. and White, Ethan P. and Moses, Melanie E. and Ernest, S. K. Morgan and Enquist, Brian J. and Charnov, Eric L.},
-doi = {10.1126/science.1123679},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Savage et al. - 2006 - Comment on The illusion of invariant quantities in life histories.pdf:pdf},
-journal = {Science},
-number = {5771},
-pages = {U1--U2},
-title = {{Comment on "The illusion of invariant quantities in life histories"}},
-volume = {312},
-year = {2006}
-}
-@article{JournalofficieldelaRepubliquefrancaise1978,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n°78-399 du 20 mars 1978 relatif, pour les d{\'{e}}partements d'outre-mer, {\`{a}} la prise en charge des frais de voyage de cong{\'{e}}s bonifi{\'{e}}s accord{\'{e}}s aux magistrats et fonctionnaires civils de l'Etat.}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=LEGITEXT000006062863},
-year = {1978}
-}
-@article{Gilbert2004,
-abstract = {A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. if there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment.},
-author = {Gilbert, Benjamin and Lechowicz, Martin J.},
-doi = {10.1073/pnas.0400814101},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gilbert, Lechowicz - 2004 - Neutrality, niches, and dispersal in a temperate forest understory.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {20},
-pages = {7651--7656},
-title = {{Neutrality, niches, and dispersal in a temperate forest understory}},
-url = {http://www.pnas.org/content/101/20/7651},
-volume = {101},
-year = {2004}
-}
-@article{Picone2009,
-abstract = {Theory predicts intense price competition results when firms cluster with rivals. Yet, strong evidence of clustering is found in previous empirical research. Researchers typically measure clustering by comparing observed location patterns to random assignment. The random assignment benchmark does not, however, account for zoning and geography and therefore might overstate the extent of strategic agglomeration. As evidence, we find that public elementary schools cluster more than random, not because of agglomeration economies, but due to demand density and limited location options. We argue that a better measurement of strategic agglomeration is to compare across product markets with similar zoning and other location restrictions but different benefits from agglomeration. We use L-function analysis of five product markets in five cities. We find that retailers with greater ability to differentiate their products are more likely to strategically cluster. {\textcopyright} 2008 Elsevier B.V. All rights reserved.},
-annote = {Cited By (since 1996):3
-Export Date: 24 May 2013
-Source: Scopus
-CODEN: IJIOD
-:doi 10.1016/j.ijindorg.2008.11.007
-Language of Original Document: English
-Correspondence Address: Ridley, D.B.; Fuqua School of Business, Duke University, Durham, NC 27708, United States; email: david.ridley@duke.edu},
-author = {Picone, Gabriel A. and Ridley, David B. and Zandbergen, Paul A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Picone, Ridley, Zandbergen - 2009 - Distance decreases with differentiation Strategic agglomeration by retailers.pdf:pdf},
-isbn = {01677187 (ISSN)},
-journal = {International Journal of Industrial Organization},
-number = {3},
-pages = {463--473},
-title = {{Distance decreases with differentiation: Strategic agglomeration by retailers}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-63449103332{\&}partnerID=40{\&}md5=95201d43d7c5093c3cb9670640c3f30f},
-volume = {27},
-year = {2009}
-}
-@book{LeBellec1997,
-author = {{Le Bellec}, Fabrice and Renard, Val{\'{e}}rie},
-isbn = {2-8-7763-050-1},
-pages = {1--189},
-publisher = {Orphie},
-title = {{Le grand livre des fruits tropicaux}},
-year = {1997}
-}
-@article{Krebs1972,
-abstract = {CHAPTER 24  Organization III: Disturbance and Nonequilibrium Communities 485 CHAPTER 25 Ecosystem Metabolism I: Primary  513 CHAPTER 26 Ecosystem Metabolism II:   537 },
-author = {Krebs, C},
-isbn = {0321604687, 9780321604682},
-journal = {Ecology. New York: Harper and Row},
-pages = {1--14},
-title = {{The Experimental Analysis of Distribution and Abundance}},
-url = {papers2://publication/uuid/6CF270B4-8486-417B-AC07-3E4BB56E8FDF{\%}5Cnhttp://www.ulb.tu-darmstadt.de/tocs/94263906.pdf{\%}5Cnpapers2://publication/uuid/6DD173AA-FBDA-47BB-B9D6-AE476B4CF94A},
-year = {1972}
-}
-@article{Arbia2001b,
-abstract = {In the present article we propose a spatial micro econometric approach$\backslash$nfor studying the geographical concentration of economic activities. We$\backslash$nanalyse the incentives to use this approach rather than the traditional$\backslash$none based on regional aggregates. As an example, we present our$\backslash$nprototypical theoretic model - to be seen as a continuous space version$\backslash$nof Krugman's concentration model - that includes birth, survival and$\backslash$ngrowth components. We present a numerical estimation of the birth model$\backslash$nfor a set of data referring to the concentration of the manufacturing$\backslash$nindustries in the San Marino Republic.},
-author = {Arbia, Giuseppe},
-doi = {10.1007/PL00013646},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia - 2001 - Modelling the Geography of Economic Activities on a Continuous Space.pdf:pdf},
-journal = {Papers in Regional Science},
-number = {4},
-pages = {411--424},
-title = {{Modelling the Geography of Economic Activities on a Continuous Space}},
-volume = {80},
-year = {2001}
-}
-@incollection{Herben2003,
-abstract = {Horizontal spatial pattern is one of the most conspicuous features of plant communities. Most air photographs of any habitat show unequal arrangement of individuals in horizontal space, aggregation of individuals belonging to one plant species, and many different types of spatial correlation if many species are involved. This horizontal spatial heterogeneity was noticed by early botanists and has spawned a large body of literature on its identification and interpretation (for a review, see [11]). Spatial patterning is one of the major research subjects in plant ecology: understanding how this ubiquitous phenomenon comes into being is likely to be one of the essential elements in understanding how plant communities are assembled and how they work. However, spatial patterns are often much noisier than many other biologically interesting patterns, highlighting the role of stochastic events that can overwhelm the underlying regularities — or questioning the existence of such regularity at all. Spatial pattern has also been invoked as having important dynamical consequences for plant communities [32, 35]. Widespread as the patterns in plant communities may be there is still no complete consensus on the processes that generate and maintain them, and on the dynamical consequences they may have. In this paper, we will briefly review current research on this subject, and try to highlight current developments in the area.},
-author = {Herben, Tom{\'{a}}{\v{s}} and Hara, Toshihiko},
-booktitle = {Morphogenesis and Patern Formation in Biological Systems: Experiments and Models},
-doi = {10.1007/978-4-431-65958-7_19},
-editor = {Sekimura, Toshio and Noji, Sumihare and Ueno, Naoto and Maini, Philip K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hans Meinhardt (auth.), Toshio Sekimura D.Sc., Sumihare Noji D.Sc., Naoto Ueno Ph.D., Philip K. Maini Ph.D. (eds.)-Morphogenesis and Pat.pdf:pdf},
-pages = {223--235},
-publisher = {Springer Japan},
-title = {{Spatial pattern formation in plant communities}},
-url = {https://link.springer.com/chapter/10.1007{\%}2F978-4-431-65958-7{\_}19},
-year = {2003}
-}
-@incollection{Whitmore1996a,
-abstract = {Introduction: The torrent of articles on forest regeneration, so-called 'gap-phase dynamics', continues unabated. The attempt to discover patterns to reduce the complexity of nature as a basis from which to make generalizations has led to the wide recognition of guilds or classes of ecologically similar tree species. The attempt to define these by Swaine and Whitmore (1988) and the subsequent debate (e.g. Platt and Strong, 1989) has contributed to this flood, see p. 8 below. Studies on aspects of gap-phase dynamics have been made and are ongoing in forests in many parts of the world (Platt and Strong, 1989) with strong concentrations in Japan (e.g. Yamamoto, 1992a,b) and North America (e.g. Canham and Marks, 1985). Part of the interest has, naturally, focused on tree seedling ecology. The present review is confined to tree seedling studies made in tropical rain forests. Many of the workers actively studying rain forest tree seedlings presented their findings at a UNESCO Workshop held in Aberdeen, Scotland, in September, 1992 (Swaine, 1995). Here those findings are set in the context of other recent work. This article does not attempt to cover all aspects comprehensively. In particular, seedling demography and functional morphology are covered elsewhere, by Lieberman (1996) and Garwood (1996). From this review various gaps in knowledge or understanding can be identified. It is suggested that future effort might profitably be directed towards them. The focus is very strongly on tropical rain forests. Tropical dry forests have attracted less recent attention (but see Hytteborn and Skarpe, 1992) and it has been suggested that in dry forests gap-phase dynamics may be less important (Swaine et al., 1990). Most of the world;s forests have many similar dynamic features but space, time and the author;s competence preclude more than a few references to work outside the humid tropics. Seed ecology is also excluded, and was outside the remit of the UNESCO Workshop. The focus here is on seedlings from germination through establishment and survival to release and growth to sapling size which, following a common foresters; convention, is taken as 2.7 in (9 feet) tall (Whitmore, 1984a).},
-address = {Paris},
-author = {Whitmore, T. C.},
-booktitle = {The Ecology of Tropical Forest Tree Seedlings},
-editor = {Swaine, M D},
-isbn = {1-85070-687-5},
-pages = {3--39},
-publisher = {UNESCO/ Parthenon Publishing},
-title = {{A review of some aspects of tropical rain forest seedling ecology with suggestions for further inquiry}},
-year = {1996}
-}
-@article{Strona2015,
-abstract = {Despite substantial recent progress, ecologists continue to search for methods of measuring the structure of ecological networks. Several studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners. Here, we introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species' tendency against sharing interacting partners) that we call ‘node segregation'. In addition, our procedure provides also a straightforward measure of modularity, that is, the tendency of a network to be compartmented into separated clusters of interacting nodes. This new analytical measure of network structure assesses the average deviation between the observed number of neighbours shared by any pair of nodes (species), and the expected number, that is computed using a probabilistic approach based on simple combinatorics. The measure can be applied to both bipartite networks (such as plant–pollinators) and unimode networks (such as food webs). We tested our approach on several sets of hypothetical and real-world networks. We demonstrate that our approach makes it possible to identify different kinds of non-random network configurations (nestedness, node segregation and modularity). In addition, we show that nestedness in ecological networks is less common than previously thought, and that most ecological networks (including the majority of mutualistic ones) tend towards patterns of segregated associations. Our analyses show that the new measure of node overlap and segregation can efficiently identify different structural patterns. The results of our analyses conducted on real networks highlight the need to carefully reconsider the assumption that ecological networks are stable due to their inherent nestedness.},
-author = {Strona, Giovanni and Veech, Joseph A.},
-doi = {10.1111/2041-210X.12395},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Strona, Veech - 2015 - A new measure of ecological network structure based on node overlap and segregation.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {8},
-pages = {907--915},
-title = {{A new measure of ecological network structure based on node overlap and segregation}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12395},
-volume = {6},
-year = {2015}
-}
-@article{Zhang2012,
-abstract = {A new nonparametric estimator of Shannon's entropy on a countable alphabet is proposed and analyzed against the well-known plug-in estimator. The proposed estimator is developed based on Turing's formula which recovers distributional characteristics on the subset of the alphabet not covered by a size-n sample. The fundamental switch in perspective brings about substantial gain in estimation accuracy for every distribution with finite entropy. In general, a uniform variance upper bound is established for the entire class of distributions with finite entropy that decays at a rate of O(ln(n)/n) compared to O([ln(n)]2/n) for the plug-in; in a wide range of subclasses, the variance of the proposed estimator converges at a rate of O(1/n); and this rate of convergence carries over to the convergence rates in mean squared errors in many subclasses. Specifically for any finite alphabet, the proposed estimator has a bias decaying exponentially in n. Several new bias-adjusted estimators are also discussed. ∗AMS},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Zhang, Zhiyi},
-doi = {10.1162/NECO_a_00266},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang - 2012 - Entropy Estimation in Turing's Perspective.pdf:pdf},
-journal = {Neural Computation},
-number = {5},
-pages = {1368--1389},
-title = {{Entropy Estimation in Turing's Perspective}},
-url = {http://dx.doi.org/10.1162/NECO{\_}a{\_}00266},
-volume = {24},
-year = {2012}
-}
-@article{Ricotta2002,
-abstract = {Most ecological diversity indices summarize the information about the relative abundances of community species without reflecting taxonomic differences between species. Nevertheless, in the environmental conservation practice, data on species abundances are generally unknown. In such cases, to summarize the conservation value of a given site, so-called ‘biological diversity' measures need to be used. Most of these measures are based on taxonomic relations among species and ignore species relative abundances. In a recent paper, Izs{\'{a}}k and Papp suggest that the quadratic entropy index (Q) is the only diversity index used to date in the ecological practice that incorporates both species relative abundances and a measure of the pairwise taxonomic differences between species in the analyzed data set. I show here that a number of traditional ecological diversity measures can be generalized to take into account a taxonomic weighting factor. Since these new indices violate part of the mathematical properties that an index should meet to be termed an ecological diversity index, I defined this new family of indices ‘weak diversity indices'.},
-author = {Ricotta, Carlo},
-doi = {10.1016/S0304-3800(01)00468-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2002 - Bridging the gap between ecological diversity indices and measures of biodiversity with Shannon's entropy comment to Iz.pdf:pdf},
-journal = {Ecological Modelling},
-number = {1},
-pages = {1--3},
-title = {{Bridging the gap between ecological diversity indices and measures of biodiversity with Shannon's entropy: comment to Izs{\'{a}}k and Papp}},
-url = {http://www.sciencedirect.com/science/article/pii/S0304380001004689},
-volume = {152},
-year = {2002}
-}
-@article{Mooers1997,
-abstract = {Inferences about macroevolutionary processes have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has led to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lenghts. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research. Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuos variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes. The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.},
-author = {Mooers, Arne {\O}. and Heard, Stephen B.},
-doi = {10.1086/419657},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mooers, Heard - 1997 - Inferring Evolutionary Process from Phylogenetic Tree Shape.pdf:pdf},
-journal = {The Quarterly Review of Biology},
-number = {1},
-pages = {31--54},
-title = {{Inferring Evolutionary Process from Phylogenetic Tree Shape}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/419657},
-volume = {72},
-year = {1997}
-}
-@article{Rauch1993,
-abstract = {When will an industry subject to agglomeration economies move from an old, high-cost site to a new, low-cost site? It is argued that history, in the form of sunk costs resulting from the operation of many firms at a site, creates a first-mover disadvantage that can prevent relocation. It is demonstrated that developers of industrial parks can partly overcome this inertia through discriminatory pricing of land over time, and empirical evidence is provided that they actually engage in such behavior. It is also shown that other aspects of developer land-sale strategy can be a source of information on the nature of interfirm externalities.},
-author = {Rauch, James E.},
-doi = {10.2307/2118410},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rauch - 1993 - Does history matter only when it matters little The case of city-industry location.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {3},
-pages = {843--867},
-title = {{Does history matter only when it matters little? The case of city-industry location}},
-url = {https://doi.org/10.2307/2118410},
-volume = {108},
-year = {1993}
-}
-@incollection{Baddeley2007,
-abstract = {spatial point patterns},
-address = {Berlin, Heidelberg},
-author = {Baddeley, Adrian J.},
-booktitle = {Stochastic Geometry},
-doi = {10.1007/3-540-38174-0},
-editor = {Weil, Wolfgang},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley - 2007 - Spatial Point Processes and their Applications.pdf:pdf},
-isbn = {9783540381747},
-pages = {1--75},
-publisher = {Springer},
-title = {{Spatial Point Processes and their Applications}},
-url = {http://link.springer.com/book/10.1007{\%}2F3-540-38174-0},
-year = {2007}
-}
-@article{Renner2013,
-abstract = {Summary Modeling the spatial distribution of a species is a fundamental problem in ecology. A number of modeling methods have been developed, an extremely popular one being MAXENT, a maximum entropy modeling approach. In this article, we show that MAXENT is equivalent to a Poisson regression model and hence is related to a Poisson point process model, differing only in the intercept term, which is scale-dependent in MAXENT. We illustrate a number of improvements to MAXENT that follow from these relations. In particular, a point process model approach facilitates methods for choosing the appropriate spatial resolution, assessing model adequacy, and choosing the LASSO penalty parameter, all currently unavailable to MAXENT. The equivalence result represents a significant step in the unification of the species distribution modeling literature.},
-author = {Renner, Ian W. and Warton, David I.},
-doi = {10.1111/j.1541-0420.2012.01824.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Renner, Warton - 2013 - Equivalence of MAXENT and Poisson Point Process Models for Species Distribution Modeling in Ecology.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {274--281},
-title = {{Equivalence of MAXENT and Poisson Point Process Models for Species Distribution Modeling in Ecology}},
-url = {http://dx.doi.org/10.1111/j.1541-0420.2012.01824.x},
-volume = {69},
-year = {2013}
-}
-@article{Baselga2012,
-abstract = {Aim Beta diversity can be partitioned into two components: dissimilarity due to species replacement and dissimilarity due to nestedness (Baselga, 2010, Global Ecology and Biogeography, 19, 134–143). Several contributions have challenged this approach or proposed alternative frameworks. Here, I review the concepts and methods used in these recent contributions, with the aim of clarifying: (1) the rationale behind the partitioning of beta diversity into species replacement and nestedness-resultant dissimilarity, (2) how, based on this rationale, numerators and denominators of indices have to match, and (3) how nestedness and nestedness-resultant dissimilarity are related but different concepts. Innovation The rationale behind measures of species replacement (turnover) dictates that the number of species that are replaced between sites (numerator of the index) has to be relativized with respect to the total number of species that could potentially be replaced (denominator). However, a recently proposed partition of Jaccard dissimilarity fails to do this. In consequence, this partition underestimates the contribution of species replacement and overestimates the contribution of richness differences to total dissimilarity. I show how Jaccard dissimilarity can be partitioned into meaningful turnover and nestedness components, and extend these new indices to multiple-site situations. Finally the concepts of nestedness and nestedness-resultant dissimilarity are discussed. Main conclusions Nestedness should be assessed using consistent measures that depend both on paired overlap and matrix filling, e.g. NODF, whereas beta-diversity patterns should be examined using measures that allow the total dissimilarity to be separated into the components of dissimilarity due to species replacement and dissimilarity due to nestedness. In the case of multiple-site dissimilarity patterns, averaged pairwise indices should never be used because the mean of the pairwise values is unable to accurately reflect the multiple-site attributes of dissimilarity.},
-author = {Baselga, Andr{\'{e}}s},
-doi = {10.1111/j.1466-8238.2011.00756.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baselga - 2012 - The relationship between species replacement, dissimilarity derived from nestedness, and nestedness.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {12},
-pages = {1223--1232},
-title = {{The relationship between species replacement, dissimilarity derived from nestedness, and nestedness}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2011.00756.x/abstract},
-volume = {21},
-year = {2012}
-}
-@article{Tilman1997,
-abstract = {Humans are modifying both the identities and numbers of species in ecosystems, but the impacts of such changes on ecosystem processes are controversial. Plant species diversity, functional diversity, and functional composition were experimentally varied in grassland plots. Each factor by itself had significant effects on many ecosystem processes, but functional composition and functional diversity were the principal factors explaining plant productivity, plant percent nitrogen, plant total nitrogen, and light penetration. Thus, habitat modifications and management practices that change functional diversity and functional composition are likely to have large impacts on ecosystem processes.},
-author = {Tilman, David and Knops, Johannes and Wedin, David and Reich, Peter and Ritchie, Mark and Siemann, Evan},
-doi = {10.1126/science.277.5330.1300},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tilman et al. - 1997 - The Influence of Functional Diversity and Composition on Ecosystem Processes.pdf:pdf},
-journal = {Science},
-number = {5330},
-pages = {1300--1302},
-title = {{The Influence of Functional Diversity and Composition on Ecosystem Processes}},
-url = {http://www.sciencemag.org/content/277/5330/1300.abstract},
-volume = {277},
-year = {1997}
-}
-@book{Wickham2014,
-author = {Wickham, Hadley},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wickham - 2014 - Advanced R.pdf:pdf},
-isbn = {978-1466586963},
-publisher = {Chapman and Hall/CRC},
-title = {{Advanced R}},
-url = {http://adv-r.had.co.nz/},
-year = {2014}
-}
-@incollection{Ottaviano2004,
-address = {Amsterdam},
-author = {Ottaviano, Gianmarco I P and Thisse, Jacques-Fran{\c{c}}ois},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ottaviano, Thisse - 2004 - Agglomeration and economic geography.pdf:pdf},
-keywords = {Ottaviano (2003a).pdf},
-mendeley-tags = {Ottaviano (2003a).pdf},
-pages = {44 p.},
-publisher = {Elsevier. North Holland},
-title = {{Agglomeration and economic geography}},
-url = {http://www.hec.unil.ch/deep/evenements/3c-combes1.pdf},
-year = {2004}
-}
-@book{Maddala1983,
-address = {Cambridge, New York},
-author = {Maddala, G. S.},
-publisher = {Cambridge University Press},
-title = {{Limited-dependent and qualitative variables in econometrics}},
-year = {1983}
-}
-@article{Majekova2016,
-abstract = {Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.},
-author = {M{\'{a}}jekov{\'{a}}, Maria and Paal, Taavi and Plowman, Nichola S. and Bryndov{\'{a}}, Michala and Kasari, Liis and Norberg, Anna and Weiss, Matthias and Bishop, Tom R. and Luke, Sarah H. and Sam, Katerina and {Le Bagousse-Pinguet}, Yoann and Lep{\v{s}}, Jan and G{\"{o}}tzenberger, Lars and {De Bello}, Francesco},
-doi = {10.1371/journal.pone.0149270},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/M{\'{a}}jekov{\'{a}} et al. - 2016 - Evaluating Functional diversity Missing trait data and the importance of species abundance structure and data t.PDF:PDF},
-journal = {PLoS ONE},
-number = {3},
-pages = {e0152532},
-title = {{Evaluating Functional diversity: Missing trait data and the importance of species abundance structure and data transformation}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149270},
-volume = {11},
-year = {2016}
-}
-@article{Guillain2010,
-abstract = {The agglomeration patterns of twenty-six manufacturing and service sectors in and around Paris in 1999 are analysed. The method used measures the intensity of spatial agglomeration and identifies the location patterns of economic sectors. First the locational Gini coefficient and Moran's I statistics of global spatial autocorrelation are computed. These provide different but complementary information about the spatial agglomeration of the sectors under study. Then exploratory spatial data analysis tools are applied. Moran scatterplots and local indicators of spatial association statistics reveal great diversity in location patterns across sectors. Reprinted by permission of Pion Limited},
-author = {Guillain, Rachel and {Le Gallo}, Julie},
-doi = {10.1068/b35038},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guillain, le Gallo - 2010 - Agglomeration and dispersion of economic activities in and around Paris An exploratory spatial data analysis.pdf:pdf},
-journal = {Environment and Planning B: Planning and Design},
-number = {6},
-pages = {961--981},
-title = {{Agglomeration and dispersion of economic activities in and around Paris: An exploratory spatial data analysis}},
-volume = {37},
-year = {2010}
-}
-@article{Wiegand2007,
-abstract = {A persistent challenge in ecology is to explain the high diversity of tree species in tropical forests. Although the role of species characteristics in maintaining tree diversity in tropical forests has been the subject of theory and debate for decades, spatial patterns in local diversity have not been analyzed from the viewpoint of individual species. To measure scale-dependent local diversity structures around individual species, we propose individual species-area relationships (ISAR), a spatial statistic that marries common species-area relationships with Ripley's K to measure the expected alpha diversity in circular neighborhoods with variable radius around an arbitrary individual of a target species. We use ISAR to investigate if and at which spatial scales individual species increase in tropical forests' local diversity (accumulators), decrease local diversity (repellers), or behave neutrally. Our analyses of data from Barro Colorado Island (Panama) and Sinharaja (Sri Lanka) reveal that individual species leave identifiable signatures on spatial diversity, but only on small spatial scales. Most species showed neutral behavior outside neighborhoods of 20 m. At short scales ({\textless}20 m), we observed, depending on the forest type, two strongly different roles of species: diversity repellers dominated at Barro Colorado Island and accumulators at Sinharaja. Nevertheless, we find that the two tropical forests lacked any key species structuring species diversity at larger scales, suggesting that "balanced" species-species interactions may be a characteristic of these species-rich forests. We anticipate our analysis method will be a starting point for more powerful investigations of spatial structures in diversity to promote a better understanding of biodiversity in tropical forests.},
-author = {Wiegand, Thorsten and Gunatilleke, C. V. Savitri and Gunatilleke, I. A. U. Nimal and Huth, Andreas},
-doi = {10.1073/pnas.0705621104},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand et al. - 2007 - How individual species structure diversity in tropical forests.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {48},
-pages = {19029--33},
-title = {{How individual species structure diversity in tropical forests.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2141902{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {104},
-year = {2007}
-}
-@article{Zhao2010,
-abstract = {The K-function is one of the most commonly used summary statistics. It plays the role for spatial point processes that the covariance function or the variogram plays for continuous observation. The asymptotic properties of the nonparametric estimation of K-function in stationary spatial point processes have been studied. However, in practice, stationary is often not a reasonable assumption. In this article, we investigate the asymptotic behaviour of the nonparametric estimation of K-function for a class of nonstationary processes.},
-annote = {ISI Document Delivery No.: 597AJ
-Times Cited: 0
-Cited Reference Count: 17
-Zhao, Jin Wang, Jinde
-TAYLOR {\&} FRANCIS LTD},
-author = {Zhao, J. and Wang, J. D.},
-doi = {10.1080/02331880903024132},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhao, Wang - 2010 - Asymptotic properties of an empirical K-function for inhomogeneous spatial point processes.pdf:pdf},
-journal = {Statistics},
-number = {3},
-pages = {261--267},
-title = {{Asymptotic properties of an empirical K-function for inhomogeneous spatial point processes}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/02331880903024132},
-volume = {44},
-year = {2010}
-}
-@article{Gignoux1999,
-abstract = {Diggle's tests of spatial randomness based on empirical distributions of interpoint distances can be performed with and without edge-effect correction. We present here numerical results illustrating that tests without the edge-effect correction proposed by Diggle (1979, Biometrics 35, 87-101) have a higher power for small sample sizes than those with correction. Ignoring the correction enables detection of departure from spatial randomness with smaller samples (down to 10 points vs. 30 points for the tests with correction). These results are confirmed by an example with ecological data consisting of maps of two species of trees in a West African savanna. Tree numbers per species per map were often less than 20. For one of the species, for which maps strongly suggest an aggregated pattern, tests without edge-effect correction enabled rejection of the null hypothesis on three plots out of five vs. on only one for the tests with correction. KEY},
-author = {Gignoux, Jacques and Duby, Camille and Barot, S{\'{e}}bastien},
-doi = {10.1111/j.0006-341X.1999.00156.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gignoux, Duby, Barot - 1999 - Comparing the performances of Diggle's test of spatial randomness for small samples with or without edge e.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {156--164},
-title = {{Comparing the performances of Diggle's test of spatial randomness for small samples with or without edge effect correction: application to ecological data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0006-341X.1999.00156.x/abstract},
-volume = {55},
-year = {1999}
-}
-@article{Baclet2008,
-abstract = {En France, la mesure de r{\'{e}}f{\'{e}}rence des in{\'{e}}galit{\'{e}}s de revenus s'appuie sur une d{\'{e}}finition du niveau de vie qui prend uniquement en compte les ressources mon{\'{e}}taires. Jusque dans un pass{\'{e}} r{\'{e}}cent, cette mesure appr{\'{e}}hendait mal les revenus du patrimoine financier et ignorait la contribution du logement au niveau de vie des individus. La prise en compte «{\'{e}}largie» des revenus du patrimoine dans la mesure des niveaux de vie modifie le paysage des in{\'{e}}galit{\'{e}}s en France. Qu'il s'agisse du patrimoine financier, dont la distribution au sein de la population est plus concentr{\'{e}}e que celle des revenus, ou de la propri{\'{e}}t{\'{e}} de la r{\'{e}}sidence principale, les compl{\'{e}}ments de ressources estim{\'{e}}s accroissent la mesure des in{\'{e}}galit{\'{e}}s globales. Les in{\'{e}}galit{\'{e}}s de niveau de vie entre les diff{\'{e}}rentes cat{\'{e}}gories socioprofessionnelles et selon l'{\^{a}}ge en sont {\'{e}}galement modifi{\'{e}}es. Le niveau de vie moyen des personnes {\^{a}}g{\'{e}}es est inf{\'{e}}rieur {\`{a}} la moyenne de la population avec la mesure standard du niveau de vie. Compte tenu du fait que le patrimoine des seniors est sup{\'{e}}rieur {\`{a}} la moyenne, la prise en compte des revenus du patrimoine am{\'{e}}liore leur niveau de vie relativement au reste la population.},
-author = {Baclet, Alexandre and Raynaud, Emilie},
-doi = {10.3406/estat.2008.7028},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baclet, Raynaud - 2008 - La prise en compte des revenus du patrimoine dans la mesure des in{\'{e}}galit{\'{e}}s(2).pdf:pdf},
-journal = {Economie et Statistique},
-number = {1},
-pages = {31--52},
-title = {{La prise en compte des revenus du patrimoine dans la mesure des in{\'{e}}galit{\'{e}}s}},
-url = {http://www.persee.fr/web/revues/home/prescript/article/estat{\_}0336-1454{\_}2008{\_}num{\_}414{\_}1{\_}7028},
-volume = {414},
-year = {2008}
-}
-@article{Whitlock2011,
-abstract = {The genetic differentiation among populations is affected by mutation as well as by migration, drift and selection. For loci with high mutation rates, such as microsatellites, the amount of mutation can influence the values of indices of differentiation such as GST and FST. For many purposes, this effect is undesirable, and as a result, new indices such as G0ST and D have been proposed to measure population differentiation. This paper shows that these new indices are not effective measures of the causes or consequences of population structure. Both G0ST and D depend heavily on mutation rate, but both are insensitive to any population genetic process when the mutation rate is high relative to the migration rate. Furthermore, D is specific to the locus being measured, and so little can be inferred about the population demography from D. However, at equilibrium, D may provide an index of whether a particular marker is more strongly affected by mutation than by migration. I argue that FST is a more important summary of the effects of population structure than D and that RST or other measures that explicitly account for the mutation process are much better than GST, G0ST,or D for highly mutable markers. Markers with lower mutation rates will often be easier to interpret.},
-author = {Whitlock, Michael C.},
-doi = {10.1111/j.1365-294X.2010.04996.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whitlock - 2011 - G'ST and D do not replace FST.pdf:pdf},
-journal = {Molecular Ecology},
-number = {6},
-pages = {1083--1091},
-title = {{G'ST and D do not replace FST}},
-url = {http://doi.wiley.com/10.1111/j.1365-294X.2010.04996.x},
-volume = {20},
-year = {2011}
-}
-@book{Theil1967,
-address = {Chicago},
-author = {Theil, H.},
-publisher = {Rand McNally {\&} Company},
-title = {{Economics and Information Theory}},
-year = {1967}
-}
-@article{Stamp1990,
-abstract = {(1) Seed dispersal distances were estimated experimentally for three species of ballistic-dispersing perennials in the understorey of Pinus palustris-Quercus laevis (longleaf-pine-turkey-oak) woodland in north-central Florida. (2) Under windless conditions, ballistic dispersal distributed seeds approximately 1 m. Ants moved the seeds 15 cm to over 8 m on average, depending on the species of ant. (3) Second-order neighbourhood analysis was used to determine the spatial pattern of adult plants. For those with patchy distributions, the number of plants patch-', patch radius and mean distance between patches were estimated. One species (Stillingia sylvatica) was positioned randomly; the others (Cnidoscolus stimulosus and Crotalaria rotundifolia) were clumped, with up to 3 and 30 individuals patch-', respectively. (4) Based on these patch measurements, ballistic seed dispersal was less than half the average distance to the nearest conspecific neighbour, and it was insufficient to ensure that seeds moved beyond the maternal patch. (5) Harvester ants (Pogonornyrmex badius) carried seeds on average 4-9 conspecific (plant) neighbours away and usually deposited seeds at the nest. In contrast to the limited range of ballistic dispersal, seed transport by harvester ants placed seeds beyond the maternal patch. The spacing of seeds appears to be facilitated by the frequent movement of harvester-ant colonies in this habitat.},
-author = {Stamp, Nancy E. and Lucas, Jeffrey R.},
-doi = {10.2307/2260886},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stamp, Lucas - 1990 - Spatial Patterns and Dispersal Distances of Explosively Dispersing Plants in Florida Sandhill Vegetation.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {589--600},
-title = {{Spatial Patterns and Dispersal Distances of Explosively Dispersing Plants in Florida Sandhill Vegetation}},
-url = {https://www.jstor.org/stable/2260886},
-volume = {78},
-year = {1990}
-}
-@article{Warwick1995,
-abstract = {We demonstrate a continuous decrease in the taxonomic distinctness of a marine assemblage along a gradient of increasing environmental contamination, in a situation where species diversity remains constant. Two indices have been employed, △ and △*, the first being a taxonomic diversity index empirically related to Shannon species diversity (H') but with an added component of taxonomic separation, and the second a measure purely of taxonomic distinctness. The values of both indices appear to be rather less influenced by sample size than does H', and markedly less sample-size dependent than other common diversity measures such as species richness and evenness. It is concluded that taxonomic distinctness may be a more sensitive univariate index of community perturbation than species diversity. We also argue that △ comes closer to a 'biodiversity' index than H', and suggest the possibility that the total genetic complement in any biome may, within limits, remain more or less constant but be partitioned differently among the hierarchy of taxonomic units, according to the age or successional stage of the assemblage.},
-author = {Warwick, R. M. and Clarke, K. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Warwick, Clarke - 1995 - New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress.pdf:pdf},
-journal = {Marine Ecology Progress Series},
-pages = {301--305},
-title = {{New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress}},
-url = {http://www.jstor.org/stable/24855596},
-volume = {129},
-year = {1995}
-}
-@article{Loreau2001,
-abstract = {Interactions between the diversity of primary producers and that of decomposers-the two key functional groups that form the basis of all ecosystems-might have major consequences on the functioning of depauperate ecosystems. I I,resent a simple ecosystem model in which primary producers (plants) and decomposers (microbes) are linked through material cycling. The model considers a diversity of plant organic compounds and a diversity of microbial species. Nutrient recycling efficiency from organic compounds to decomposers is then the key parameter that controls ecosystem processes (primary productivity, secondary productivity, producer biomass and decomposer biomass). The model predicts that microbial diversity has a positive effect on nutrient recycling efficiency and ecosystem processes through either greater intensity of microbial exploitation of organic compounds or functional niche complementarity, much like in plants. Microbial niche breadth and overlap should not affect ecosystem processes unless they increase the number of organic compounds that are decomposed. In contrast, the model predicts that plant organic compound diversity can only have a negative effect or, at best, no effect on ecosystem processes, at least ill a constant environment. This creates a tension between the effects of plant diversity and microbial diversity on ecosystem functioning, which may explain some recent experimental results.},
-author = {Loreau, Michel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau - 2001 - Microbial diversity, producer-decomposer interactions and ecosystem processes a theoretical model.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {1464},
-pages = {303--309},
-title = {{Microbial diversity, producer-decomposer interactions and ecosystem processes: a theoretical model}},
-url = {http://www.jstor.org/stable/3067571},
-volume = {268},
-year = {2001}
-}
-@article{Diggle1987,
-abstract = {The paper develops a nonparametric estimator for the class of pairwise-interaction point processes. The estimator is based on an approximation in statistical physics due to Percus and Yevick, which relates the interaction function of a pairwise-interaction point process to its second-order statistics via an integral equation. The results of a simulation study are presented.},
-author = {Diggle, Peter J. and Gates, David J. and Stibbard, Alyson},
-doi = {10.1093/biomet/74.4.763},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle, Gates, Stibbard - 1987 - A Nonparametric Estimator for Pairwise-Interaction Point Processes.pdf:pdf},
-journal = {Biometrika},
-number = {4},
-pages = {763--770},
-title = {{A Nonparametric Estimator for Pairwise-Interaction Point Processes}},
-url = {https://academic.oup.com/biomet/article-abstract/74/4/763/280532/A-nonparametric-estimator-for-pairwise-interaction},
-volume = {74},
-year = {1987}
-}
-@misc{Kourilsky1992,
-author = {Kourilsky, Fran{\c{c}}ois},
-editor = {CNRS},
-title = {{D{\'{e}}cision du directeur g{\'{e}}n{\'{e}}ral n° 920368SOSI du 28 octobre 1992 modifi{\'{e}}e relative {\`{a}} la constitution, la composition, la comp{\'{e}}tence et au fonctionnement des conseils de laboratoire des structures op{\'{e}}rationnelles de recherche et des structures op{\'{e}}rationnelle}},
-url = {http://www.sg.cnrs.fr/daj/textes/reglementation/textes/dec{\_}920368.htm},
-volume = {920368SOSI},
-year = {1992}
-}
-@book{Harville2008,
-address = {New York},
-author = {Harville, David A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harville - 2008 - Matrix algebra from a statistician's perspective.pdf:pdf},
-isbn = {9780387783567},
-pages = {1--634},
-publisher = {Springer Science+Business Media},
-title = {{Matrix algebra from a statistician's perspective}},
-url = {http://books.google.com/books?hl=en{\&}lr={\&}id=kZGBQijgGV8C{\&}oi=fnd{\&}pg=PR5{\&}dq=Matrix+Algebra+From+a+Statistician{\%}2527s+Perspective{\&}ots=LT0vRbb3Eq{\&}sig=i-Xk9jn0qvfQ{\_}CdrJ5c5dUtjGu4},
-year = {2008}
-}
-@article{Zhang2010,
-abstract = {It is shown in this paper that the parameters of a multinomial distribution may be re-parameterized as a set of generalized Simpson's diversity indices. There are two important elements in the generalization: (1) Simpson's diversity index is extended to populations with infinite species; (2) weighting schemes are incorporated. A class of unbiased estimators for the generalized Simpson's biodiversity indices is proposed. Asymptotic normality is established for the estimators. Both the unbiasedness and the asymptotic normality of the estimators hold for all three cases of the number of species in the population: infinite, finite and known, and finite but unknown. In the case of a population with a finite number of species, known or unknown, it is also established that the proposed estimators are uniformly minimum variance unbiased and are asymptotically efficient. {\textcopyright} 2009 Elsevier B.V. All rights reserved.},
-annote = {Cited By (since 1996):5
-Export Date: 25 March 2014
-Source: Scopus},
-author = {Zhang, Zhiyi and Zhou, Jun},
-doi = {10.1016/j.jspi.2009.12.023},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Zhou - 2010 - Re-parameterization of multinomial distributions and diversity indices.pdf:pdf},
-journal = {Journal of Statistical Planning and Inference},
-number = {7},
-pages = {1731--1738},
-title = {{Re-parameterization of multinomial distributions and diversity indices}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77949275741{\&}partnerID=40{\&}md5=0749f62b752c9a1a3c2757651790d7d2},
-volume = {140},
-year = {2010}
-}
-@article{Gao2014,
-abstract = {We consider LM tests for spatial correlations in the spatial error model (SEM) and spatial autore- gressive model (SAM) with randomly missing data in the dependent variable. We derive the for- mulas of the LM test statistics and provide finite sample performance of the LM tests through Monte Carlo experiments.},
-author = {Gao, Jing and Wang, Wei},
-doi = {10.4236/tel.2014.48079},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gao, Wang - 2014 - Testing for Spatial Correlations with Randomly Missing Observations in the Dependent Variable.pdf:pdf},
-journal = {Theoretical Economics Letters},
-pages = {623--633},
-title = {{Testing for Spatial Correlations with Randomly Missing Observations in the Dependent Variable}},
-url = {http://www.scirp.org/journal/PaperInformation.aspx?paperID=50304},
-volume = {4},
-year = {2014}
-}
-@article{Ripley1977,
-abstract = {Spatial point processes may be analysed at two levels. Quadrat and distance methods were designed for the sampling of a population in the field. In this paper we consider those situations in which a map of a spatial pattern has been produced at some cost and we wish to extract the maximum possible information. We review the stochastic models which have been proposed for spatial point patterns and discuss methods by which the fit of such a model can be tested. Certain models are shown to be the equilibrium distributions of spatial-temporal stochastic processes. The theory is illustrated by several case studies.},
-author = {Ripley, Brian D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1977 - Modelling Spatial Patterns.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {172--212},
-title = {{Modelling Spatial Patterns}},
-url = {http://www.jstor.org/stable/2984796},
-volume = {39},
-year = {1977}
-}
-@article{Arevalo2003,
-abstract = {Spatial patterns are important characteristics of the forest and they can reveal such things as successional status and ecological characteristics of the species. We tested the hypothesis that spatial distribution will be different, depending on whether the species is intolerant or tolerant to shade. We assessed the spatial distribution of trees ({\textgreater} 4 cm dbh) and juveniles in eight laurel forest plots. A univariate spatial analysis ( performed with Ripley's K-1) showed that all tree species have significant aggregation at short distances (2 m). Nevertheless, two groups of species could be differentiated: Erica scoparia, Myrica faya and Ilex canariensis showed a tendency for aggregation at large distances (larger than 6 m) while L. azorica and Prunus lusitanica showed aggregation only at shorter distances. Ripley's Bivariate K-1,K-2 analyses showed no significant differences in the spatial distribution of analyzed species pairs from a null model. Only Laurus azorica had a sufficient sample size for analysis of juvenile distribution. A univariate analysis revealed that L. azorica seedlings (stems {\textless} 50 cm high) were clumped in some plots up to 5 m, but this was not consistent. Saplings (stems {\textgreater} 50 cm high and {\textless} 4 cm dbh) did not show strong clumping even at short distances. L. azorica saplings had no significant aggregation with, nor repulsion from, adults of the same or different species. Spatial patterns of the species should be considered in the development of restoration plans of the laurel forest 90{\%} of which has disappeared or been intensively disturbed on Tenerife Island.},
-annote = {Article
-English
-PLANT ECOL
-622RA},
-author = {Ar{\'{e}}valo, Jos{\'{e}} Ram{\'{o}}n and Fern{\'{a}}ndez-Palacios, Jos{\'{e}} Mar{\'{i}}a},
-doi = {10.1023/A:1021490715660},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ar{\'{e}}valo, Fern{\'{a}}ndez-Palacios - 2003 - Spatial patterns of trees and juveniles in a laurel forest of Tenerife, Canary Islands.pdf:pdf},
-journal = {Plant Ecology},
-number = {1},
-pages = {1--10},
-title = {{Spatial patterns of trees and juveniles in a laurel forest of Tenerife, Canary Islands}},
-url = {https://link.springer.com/article/10.1023/A:1021490715660},
-volume = {165},
-year = {2003}
-}
-@article{Neyman1958,
-abstract = {THE basic hypothesis underlying current deterministic cosmologies, namely the so-called cosmological principle, can be stated precisely only in terms of probabilistic concepts. Consequently, considerable progress and aesthetic gain may be expected if determinism is abandoned and replaced by a frank probabilistic treatment of cosmology. This requires the adoption of the view that the Universe is a realization of a stochastic process which is stationary in the three (spatial) co-ordinates (cosmological principle) and possibly also stationary in the fourth (time) co-ordinate ("perfect" cosmological principle). Two examples are given of problems relevant to deterministic cosmological theories that elude deterministic treatment, but lend themselves to an indeterministic statistical study.},
-author = {Neyman, Jerzy and Scott, Elizabeth L},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Neyman, Scott - 1958 - Statistical Approach to Problems of Cosmology.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {1--43},
-title = {{Statistical Approach to Problems of Cosmology}},
-url = {http://www.jstor.org/stable/2983905},
-volume = {20},
-year = {1958}
-}
-@article{Shen2013,
-abstract = {Analysis of the phylogenetic similarity of co-occurring species at different spatial scales is increasingly used for decoding community assembly rules. Here, we integrated the analysis of phylobetadiversity and marked point pattern analysis to yield a new metric, the phylogenetic mark correlation function, kd(r), to quantify spatial phylogenetic structure of fully stem-mapped communities. * kd(r) is defined as the expected phylogenetic distance of two heterospecifics separated by spatial distance r, and normalized with the expected phylogenetic distance of two heterospecifics taken randomly from a study area. It measures spatial phylogenetic turnover relative to spatial species turnover and is closely related with the spatially explicit Simpson index. * We used simulated fully stem-mapped plant communities with known spatial phylogenetic structures to assess type I and II errors of the phylogenetic mark correlation function kd(r) under a null model of random phylogenetic spatial structure, and to test the ability of the kd(r) to detect scale-dependent signals of phylogenetic spatial structure. We also compared the performance of the kd(r) with two existing measures of phylobetadiversity that have been previously used to analyse fully stem-mapped plots. Finally, we explored the spatial phylogenetic structure of a 24-ha fully stem-mapped subtropical forest in China. * Simulation tests showed that the new metric yielded correct type I and type II errors and accurately detected the spatial scales at which various processes (e.g. habitat filtering and competition) were invoked to generate spatial phylogenetic structures. The power of the kd(r) was not affected by a phylogenetic signal in species abundance and different topologies of the phylogenetic tree. * Replacing phylogenetic distance by functional distance allows for application of the kd(r) to estimate spatial correlations in functional community structure. Thus, the kd(r) allows trait and phylogenetic structure to be analysed in the same framework. The phylogenetic mark correlation function is a powerful and accurate tool for revealing scale-dependent phylogenetic/functional footprints in community assemblages and allows ecologists to keep up with the increasingly available data of fully stem-mapped plots, functional traits and community phylogenies.},
-author = {Shen, Guochun and Wiegand, Thorsten and Mi, Xiangcheng and He, Fangliang},
-doi = {10.1111/2041-210X.12119},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shen et al. - 2013 - Quantifying spatial phylogenetic structures of fully stem-mapped plant communities.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shen et al. - 2013 - Quantifying spatial phylogenetic structures of fully stem-mapped plant communities.doc:doc},
-journal = {Methods in Ecology and Evolution},
-number = {12},
-pages = {1132--1141},
-title = {{Quantifying spatial phylogenetic structures of fully stem-mapped plant communities}},
-url = {http://dx.doi.org/10.1111/2041-210X.12119},
-volume = {4},
-year = {2013}
-}
-@article{Gould1979,
-abstract = {Students of allometric growth and the species-area curve have favored the same mathematical expression, the power function, in their work. Allometricians, after much debate and error, derived satisfactory interpretations for the parameters of this function. The coefficient proved difficult because it is not invariant under change of scale and often makes no biological sense as the value of y (number of species) when x equals 1 unit. Ecologists have fallen into the same traps that plagued allometricians 30 yr ago, but have been unaware that the problems had been solved by their sister subdiscipline. Coefficients of power functions should not be neglected or ignored by ecologists (more often than not, they are not reported at all). When slopes are constant in families of related curves-a common situation in the species-area literature where slopes are so often near 0.25-ratios of coefficients are constant at all values of x (area): They record a size-independent invariant within a system. I present several invariants, previously unrecognized or identified more circuitously in other ways.},
-author = {Gould, Stephen Jay},
-doi = {10.1086/283482},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gould - 1979 - An Allometric Interpretation of Species-Area Curves The Meaning of the Coefficient.pdf:pdf},
-journal = {The American Naturalist},
-number = {3},
-pages = {335--343},
-title = {{An Allometric Interpretation of Species-Area Curves: The Meaning of the Coefficient}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/283482},
-volume = {114},
-year = {1979}
-}
-@article{Ricotta2005b,
-abstract = {Biological diversity would apparently seem the most intuitive and easily studied of all the ecological concepts. However, in practice biodiversity has suffered from great number of definitions that vary with the specific needs of the different researchers, thus making it extremely confusing as an ecological concept. In this paper, I shortly review the concept of biodiversity showing that there exists a substantial ambiguity among ecologists as far as biodiversity conceptualization and evaluation is concerned. I conclude that, due to this major disagreement on its very nature, biodiversity may be defined simply as a set of multivariate summary statistics for quantifying different characteristics of community structure.},
-annote = {Cited By (since 1996):50
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: ABIOA
-PubMed ID: 15906141
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1007/s10441-005-7001-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2005 - Through the jungle of biological diversity.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {1},
-pages = {29--38},
-title = {{Through the jungle of biological diversity}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-20044387065{\&}partnerID=40{\&}md5=21e903ff55b1346c331646b0dfba4149},
-volume = {53},
-year = {2005}
-}
-@article{Clark1984,
-abstract = {As a partial explanation for the maintenance of high tree diversity in wet tropical forests, Janzen (1970) and Connell (1971) independently hypothesized that natural enemies act to increase spacing within these tree populations through disproportionately high attack on progeny near adults. Both authors also hypothesized a minimum critical distance effect, because of 100{\%} progeny mortality within a given distance of adults. We describe the necessary and sufficient conditions for testing these hypotheses, and show that attempts to evaluate them have been hampered by use of the inappropriate standard of regular spacing. Data describing the spacing dynamics of Dipteryx panamensis, a rain forest canopy tree, support both hypotheses. From 7 mo to 2 yr postgermination, seedling survival was positively correlated with distance to adult and negatively correlated with local conspecific seedling density. Partial correlation was used to separate the effects of density and distance, and it was shown that seedling density was the only significant factor in this case. Older juveniles and saplings occurred at greater distances from the nearest conspecific adult than did 1980 seedlings. No seedlings or juveniles survived within 8 m of an adult bole. A review of 24 data sets on tropical woody plants showed that most evidence indicates either density-dependence or distance-dependence in progeny mortality, as hypothesized by Janzen and Connell. Some positive evidence also exists for the minimum critical distance effect for tropical trees. In most of the cases involving seedling mortality, however, alternative causal factors such as intracohort competition or allelopathy were not ruled out. Before generalizations can be made about this process in tropical forests, carefully designed studies are needed on more populations of tropical trees.},
-author = {Clark, Deborah and Clark, David B},
-doi = {10.1086/284316},
-isbn = {00030147},
-issn = {0003-0147},
-journal = {The American Naturalist},
-number = {6},
-pages = {769--788},
-pmid = {523},
-title = {{Spacing Dynamics of a Tropical Rain Forest Tree: Evaluation of the Janzen-Connell Model}},
-url = {http://www.jstor.org/stable/2461300},
-volume = {124},
-year = {1984}
-}
-@article{MacArthur1960,
-abstract = {1. A distinction is made between opportunistic and equilibrium species. 2. There is little ecological interest in the relative abundances of opportunistic species, but such species abundances should frequently have a log-normal distribution. 3. The relative abundances of equilibrium species are of considerable ecological interest and frequently can be deduced from the assumption that increase in one species population results in a roughly equal decrease in the populations of other species. To make the formulae well-defined it is necessary to assume that the census-taker has sampled a small area and thus achieved a certain sort of randomness. 4. For bird populations, at least, discrepancies between observations and predictions are negligible except when the censused area is compounded from different habitats. The discrepancy is then partly due to the fact that common species in one habitat are more likely to be present in adjacent habitats than are rate ones.},
-author = {MacArthur, Robert H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacArthur - 1960 - On the relative abundance of species.pdf:pdf},
-journal = {American Naturalist},
-number = {874},
-pages = {25--36},
-title = {{On the relative abundance of species}},
-url = {http://www.jstor.org/stable/2458395},
-volume = {94},
-year = {1960}
-}
-@article{Favrichon1994,
-abstract = {L'analyse statistique, par des m{\'{e}}thodes de classification, des donn{\'{e}}es quantitatives relatives au d{\'{e}}veloppement v{\'{e}}g{\'{e}}tatif des esp{\`{e}}ces arbor{\'{e}}es d'une for{\^{e}}t primaire de Guyanne fran{\c{c}}aise, permet de d{\'{e}}finir 5 groupes fonctionnels d'esp{\`{e}}ces. Ces groupes sont caract{\'{e}}ris{\'{e}}s par des valeurs de dimension potentielle et de sensibilit{\'{e}} {\`{a}} la lumi{\`{e}}re pour leur croissance en diam{\`{e}}tre au sein d'un peuplement adulte. On distingue les esp{\`{e}}ces tol{\'{e}}rantes d'{\'{e}}tages inf{\'{e}}rieurs et de la vo{\^{u}}te, semi-tol{\'{e}}rantes {\'{e}}mergentes et h{\'{e}}liophiles de sous-{\'{e}}tage et de la vo{\^{u}}te. La prise en compte de param{\`{e}}tres biologiques relatifs en particulier aux stades plus jeunes de d{\'{e}}veloppement (diss{\'{e}}mination, sensibilit{\'{e}} des plantules {\`{a}} la lumi{\`{e}}re) permet de montrer la validit{\'{e}} et des limites {\'{e}}cologiques de ces regroupements. Ces groupes seront utilis{\'{e}}s ensuite dans un mod{\`{e}}le de dynamique de population},
-author = {Favrichon, Vincent},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Favrichon - 1994 - Classification des esp{\`{e}}ces arbor{\'{e}}es en groupes fonctionnels en vue de la r{\'{e}}alisation d'un mod{\`{e}}le de dynamique de peup.pdf:pdf},
-journal = {Revue d'Ecologie (La Terre et la Vie)},
-number = {4},
-pages = {379--403},
-title = {{Classification des esp{\`{e}}ces arbor{\'{e}}es en groupes fonctionnels en vue de la r{\'{e}}alisation d'un mod{\`{e}}le de dynamique de peuplement en for{\^{e}}t guyanaise}},
-url = {http://documents.irevues.inist.fr/handle/2042/54782},
-volume = {49},
-year = {1994}
-}
-@article{Wilsey2010,
-author = {Wilsey, Brian J.},
-doi = {doi:10.1890/09-0351.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilsey - 2010 - An empirical comparison of beta diversity indices in establishing prairies.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1984--1988},
-title = {{An empirical comparison of beta diversity indices in establishing prairies}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-0351.1},
-volume = {91},
-year = {2010}
-}
-@article{Barone1998,
-abstract = {1. To assess the degree of herbivore host-specificity in the moist tropical forest on Barro Colourado Island, Panama, I conducted an extensive series of feeding trials on the common insect herbivores from 10 tree species. 2. The herbivores were offered leaves from both congeneric and confamilial plant species to their known host species, as well as leaves from the most abundant tree species in the forest. 3. The amount of damage caused by these herbivores to young, expanding leaves was also measured on nine of the tree species. 4. Of 35 herbivores species (seven Coleoptera, one Orthoptera, 38 Lepidoptera), 26{\%} were specialized to a single plant species, 22{\%} were limited to feeding on a single genus and 37{\%} were able to feed on several genera within a single family. The remaining 15{\%} were generalists, able to feed from several different plant families. 5. The causes of leaf damage varied extensively across the tree species. On average, specialist herbivores caused 58{\%} of the damage to young leaves, generalists herbivores 8{\%} and fungal pathogens 34{\%}. For four of the tree species, pathogens were the most important cause of leaf damage. 6. In this forest, most chewing herbivores appear to have fairly narrow diets, and these specialists are responsible for most of the insect herbivory.},
-author = {Barone, John A.},
-doi = {10.1046/j.1365-2656.1998.00197.x},
-journal = {Journal of Animal Ecology},
-number = {3},
-pages = {400--409},
-title = {{Host-specificity of folivorous insects in a moist tropical forest}},
-volume = {67},
-year = {1998}
-}
-@article{Clarke2001,
-abstract = {A further biodiversity index is proposed, based on taxonomic (or phylogenetic) relatedness of species, namely the 'variation in taxonomic distinctness' (VarTD, Lambda (+)) between every pair of species recorded in a study. It complements the previously defined 'average taxonomic distinctness' (AvTD, Delta (+)), which is the mean path length through the taxonomic tree connecting every pair of species in the list. VarTD is simply the variance of these pairwise path lengths and reflects the unevenness of the taxonomic tree. For example, a species list in which there are several different orders represented only by a single species, but also some genera which are very species-rich, would give a high Lambda (+) by comparison with a list (of equivalent Delta (+)) in which all species tended to be from different families but the same order. VarTD is shown to have the same desirable sampling properties as AvTD, primarily a lack of dependence of its mean value on the sample size (except for unrealistically small samples). Such unbiasedness is of crucial importance in making valid biodiversity comparisons between studies at different locations or times, with differing or uncontrolled degrees of sampling effort, This feature is emphatically not shared by indices related to species richness and also not by properties of the phylogeny adapted from proposals in other, conservation contexts, such as 'average phylogenetic diversity' (AvPD, Phi (+)). As with AvTD, the VarTD statistic for any local study can be tested for 'departure from expectation', based on a master taxonomy for that region, by constructing a simulation distribution from random subsets of the master list. The idea can be extended to summarising the joint distribution of AvTD and VarTD, so that values from real data sets are compared with a fitted simulation 'envelope' in a 2 d (Delta (+), Lambda (+)) plot. The methodology is applied to 14 species lists of free-living marine nematodes, and related to a master list for UK waters. The combination of AvTD and VarTD picks out, in different ways, some degraded locations (low Delta (+), low to normal Lambda (+)) and the pristine island fauna of the Scillies (normal Delta (+), high Lambda (+)). The 2 indices are also demonstrated to be measuring effectively independent features of the taxonomic tree, at least for this faunal group (although it is shown theoretically that this will not always be the case). The combination of Delta (+) and Lambda (+) is therefore seen to provide a statistically robust summary of taxonomic (or phylogenetic) relatedness patterns within an assemblage, which has the potential to be applied to a wide range of historical data in the form of simple species lists.},
-annote = {Clarke, KR Warwick, RM},
-author = {Clarke, K. R. and Warwick, R. M.},
-doi = {10.3354/meps216265},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clarke, Warwick - 2001 - A further biodiversity index applicable to species lists variation in taxonomic distinctness.pdf:pdf},
-journal = {Marine Ecology-Progress Series},
-pages = {265--278},
-title = {{A further biodiversity index applicable to species lists: variation in taxonomic distinctness}},
-volume = {216},
-year = {2001}
-}
-@article{Hastings1982,
-author = {Hastings, Steven E. and Goode, Frank M.},
-doi = {10.1111/j.1468-2257.1982.tb00385.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hastings, Goode - 1982 - Improved Measures of Industrial Location Factors.pdf:pdf},
-journal = {Growth and Change},
-number = {4},
-pages = {25--31},
-title = {{Improved Measures of Industrial Location Factors}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1468-2257.1982.tb00385.x/abstract},
-volume = {13},
-year = {1982}
-}
-@article{Hwang2014,
-abstract = {Good-Turing frequency estimation (Good, ) is a simple, effective method for predicting detection probabilities of objects of both observed and unobserved classes based on observed frequencies of classes in a sample. The method has been used widely in several disciplines, such as information retrieval, computational linguistics, text recognition, and ecological diversity estimation. Nevertheless, existing studies assume sampling with replacement or sampling from an infinite population, which might be inappropriate for many practical applications. In light of this limitation, this article presents a modification of the Good-Turing estimation method to account for finite population sampling. We provide three practical extensions of the modified method, and we examine performance of the modified method and its extensions in simulation experiments.},
-author = {Hwang, Wen-Han and Lin, Chih-Wei and Shen, Tsung-Jen},
-doi = {10.1002/bimj.201300168},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hwang, Lin, Shen - 2014 - Good-Turing frequency estimation in a finite population.pdf:pdf},
-journal = {Biometrical journal},
-number = {2},
-pages = {321--339},
-title = {{Good-Turing frequency estimation in a finite population}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/25394337},
-volume = {57},
-year = {2014}
-}
-@article{Veech2010a,
-abstract = {Ecologists have traditionally viewed the total species diversity within a set of communities as the product of the average diversity within a community (alpha) and the diversity among the communities (beta). This multiplicative concept of species diversity contrasts with the lesser known idea that alpha and beta-diversities sum to give the total diversity. This additive partitioning of species diTersity is nearly as old as the multiplicative concept, yet ecologists are just now beginning to use additive partitioning to examine patterns of species diversity. In this review we discuss why additive partitioning remained ‘‘hidden'' until just a few years ago. The rediscovery of additive partitioning has expanded the way in which ecologists define and measure beta-diversity. Beta diversity is no longer relegated to describing change only along an environmental gradient. Through additive partitioning, beta-diversity is explicitly an average amount of diversity just as is alpha-diversity. We believe that the additive partitioning of diversity into alpha and beta components will continue to become more widely used because it allows for a direct comparison of alpha- and beta-diversities. It also has particular relevance for testing ecological theory concerned with the determinants of species diversity at multiple spatial scales and potential applications in conservation biology},
-author = {Veech, Joseph A. and Crist, Thomas O.},
-doi = {doi:10.1890/08-1727.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veech, Crist - 2010 - Diversity partitioning without statistical independence of alpha and beta.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1964--1969},
-title = {{Diversity partitioning without statistical independence of alpha and beta}},
-url = {http://www.esajournals.org/doi/abs/10.1890/08-1727.1},
-volume = {91},
-year = {2010}
-}
-@incollection{James1961,
-address = {Berkeley, California},
-author = {James, W. and Stein, Charles},
-booktitle = {Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability},
-editor = {Neyman, Jerzy},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/James, Stein - 1961 - Estimation with Quadratic Loss.pdf:pdf},
-pages = {361--379},
-publisher = {University of California Press},
-title = {{Estimation with Quadratic Loss}},
-volume = {1},
-year = {1961}
-}
-@article{Gregorius2010,
-abstract = {Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective) numbers of trait states (types). Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, -diversity and fixation (inadvertently called differentiation) are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST ) refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.3390/d2030370},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 2010 - Linking Diversity and Differentiation.pdf:pdf},
-journal = {Diversity},
-number = {3},
-pages = {370--394},
-title = {{Linking Diversity and Differentiation}},
-url = {http://www.mdpi.com/1424-2818/2/3/370/},
-volume = {2},
-year = {2010}
-}
-@article{Esty1982,
-abstract = {The coverage of a random sample from a multinomial population is defined to be the sum of the probabilities of the observed classes. The problem is to estimate the coverage of a random sample given only the number of classes observed exactly once, twice, etc. This problem is related to the problem of estimating the number of classes in the population. Non-parametric confidence intervals are given when the coverage is low such that a Poisson approximation holds. These intervals are related to a coverage estimator of Good (1953).},
-author = {Esty, Warren W},
-doi = {10.2307/2240510},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Esty - 1982 - Confidence Intervals for the Coverage of Low Coverage Samples.pdf:pdf},
-journal = {The Annals of Statistics},
-number = {1},
-pages = {190--196},
-title = {{Confidence Intervals for the Coverage of Low Coverage Samples}},
-url = {http://www.jstor.org/stable/2240510},
-volume = {10},
-year = {1982}
-}
-@article{Genet2014,
-abstract = {The spatial structure of complex forest stands results from competitive interactions among trees which is one of the most important ecological processes influencing forest development. The aim of the study is to incorporate in a new class of random point process models a coherent representation of the competition process driving forest stand dynamics to establish a direct link between pattern and ecological processes. The resulting area-saturation model was defined by a set statistic characterised by overlapping discs representing tree interactions. Unlike previous approaches, this new spatial model has the advantage of allowing a straightforward interpretation of its parameters in terms of inter-tree competition. A 60. m. ×. 60. m plot of even-aged Scots pines was used to illustrate the potential of this approach in modelling the spatial structure of a plant community. The social status of each tree was taken into account, leading to a multivariate point pattern exhibiting various spatial properties (regularity, clustering and randomness) at different scales. We considered a hierarchical structure of interactions to account for the fact that competition for light is size-asymmetric. According to the analysis, the generalised area-saturation model has the required flexibility to capture complex spatial tree patterns. {\textcopyright} 2014 Elsevier B.V.},
-author = {Genet, Astrid and Grabarnik, Pavel and Sekretenko, Olga and Pothier, David},
-doi = {10.1016/j.ecolmodel.2014.06.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Genet et al. - 2014 - Incorporating the mechanisms underlying inter-tree competition into a random point process model to improve spatia.pdf:pdf},
-journal = {Ecological Modelling},
-pages = {143--154},
-title = {{Incorporating the mechanisms underlying inter-tree competition into a random point process model to improve spatial tree pattern analysis in forestry}},
-url = {http://dx.doi.org/10.1016/j.ecolmodel.2014.06.002},
-volume = {288},
-year = {2014}
-}
-@article{Gattone2009,
-abstract = {Diversity plays a central role in ecological theory and its conservation and man- agement are important issues for the wellbeing and stability of ecosystems. The aim of this work is to provide a reliable theoretical framework for performing statistical analysis on eco- logical diversity by means of the joint use of diversity profiles and functional data analysis.We point out that ecological diversity is a multivariate concept as it is a function of the relative abundances of species in a biological community.For this, several researchers have suggested using parametric families of indices of diversity for obtaining more information from the data. Patil and Taillie introduced the concept of intrinsic diversity ordering which can be determined by using the diversity profile. It may be noted that the diversity profile is a non-negative and convex curve which consists of a sequence of measurements as a function of a given parame- ter. Thus, diversity profiles can be explained through a process that is described in a functional setting. Recent developments in environmental studies have focused on the opportunity to eval- uate community diversity changes over space and/or correlation of diversity with environmental characteristics. For this, we develop an innovative analysis of diversity based on a functional data approach. Whereas conventional statistical methods process data as a sequence of indi- vidual observations, functional data analysis is designed to process a collection of functions or curves. Moreover, unconstrained models may lead to negative and/or non-convex estimates for the diversity profiles. To overcome this problem, a transformation is proposed which can be constrained to be non-negative and convex.We focus on some applications showing how functional data analysis provides an alternative way of understanding biological diversity and its interaction with natural and/or human factors. Keywords:},
-author = {Gattone, Stefano A. and {Di Battista}, Tonio},
-doi = {10.1111/j.1467-9876.2009.00646.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gattone, Di Battista - 2009 - A functional approach to diversity profiles.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
-month = {may},
-number = {2},
-pages = {267--284},
-title = {{A functional approach to diversity profiles}},
-url = {http://doi.wiley.com/10.1111/j.1467-9876.2009.00646.x},
-volume = {58},
-year = {2009}
-}
-@article{Beguinot2014,
-abstract = {Anne Chao proposed a very popular, nonparametric estimator of the species richness of a community, on the basis of a limited size sampling of this community. This expression was originally derived on a statistical basis as a lower-bound estimate of the number of missing species in the sample and provides accordingly a minimal threshold for the estimation of the total species richness of the community. Hereafter, we propose an alternative, algebraic derivation of Chao's estimator, demonstrating thereby that Chao's formulation may also provide centered estimates (and not only a lower bound threshold), provided that the sampled communities satisfy a specific type of SAD (species abundance distribution). This particular SAD corresponds to the case when the number of unrecorded species in the sample tends to decrease exponentially with increasing sampling size. It turns out that the shape of this “ideal” SAD often conforms approximately to the usually recorded types in nature, such as “log-normal” or “broken-stick.”. Accordingly, this may explain why Chao's formulation is generally recognized as a particularly satisfying nonparametric estimator.},
-author = {B{\'{e}}guinot, Jean},
-doi = {10.1155/2014/847328},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/B{\'{e}}guinot - 2014 - An Algebraic Derivation of Chao ' s Estimator of the Number of Species in a Community Highlights the Condition Allowin.pdf:pdf},
-journal = {International Scholarly Research Notices},
-number = {Article ID 847328},
-title = {{An Algebraic Derivation of Chao ' s Estimator of the Number of Species in a Community Highlights the Condition Allowing Chao to Deliver Centered Estimates}},
-url = {http://dx.doi.org/10.1155/2014/847328},
-volume = {2014},
-year = {2014}
-}
-@article{Baraloto2012a,
-abstract = {1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. Wemeasured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. Wealso generated a datedmolecular phylogenetic tree based onDNAsequencing of two plastid loci (rbcL and matK) comprising 97{\%}of the individuals and 91{\%}of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis.Weprovide themost comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems. Key-words:},
-author = {Baraloto, Christopher and Hardy, Olivier J. and Paine, C. E. Timothy and Dexter, Kyle G. and Cruaud, Corinne and Dunning, Luke T. and Gonzalez, Mailyn-Adriana and Molino, Jean-Fran{\c{c}}ois and Sabatier, Daniel and Savolainen, Vincent and Chave, J{\'{e}}r{\^{o}}me},
-doi = {10.1111/j.1365-2745.2012.01966.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2012 - Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {690--701},
-title = {{Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities}},
-url = {http://doi.wiley.com/10.1111/j.1365-2745.2012.01966.x},
-volume = {100},
-year = {2012}
-}
-@incollection{Ripley1987,
-address = {Berlin},
-author = {Ripley, Brian D.},
-booktitle = {Developments in numerical ecology},
-editor = {Legendre, Pierre and Legendre, L},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1987 - Spatial point pattern analysis in ecology.pdf:pdf},
-pages = {407--429},
-publisher = {Springer},
-title = {{Spatial point pattern analysis in ecology}},
-year = {1987}
-}
-@article{Harris1954,
-author = {Harris, Chauney D.},
-doi = {10.1080/00045605409352140},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harris - 1954 - The Market as a Factor in the Localization of Industry in the United States.pdf:pdf},
-journal = {Annals of the Association of American Geographers},
-number = {4},
-pages = {315--348},
-title = {{The Market as a Factor in the Localization of Industry in the United States}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/00045605409352140},
-volume = {44},
-year = {1954}
-}
-@book{Czekanowski1913,
-abstract = {Document introuvable.},
-address = {Warsaw},
-author = {Czekanowski, Jan},
-publisher = {Towarzystwo Naukowe Warszawskie},
-title = {{Zarys metod statystycznych w zastosowaniu do antropologii}},
-year = {1913}
-}
-@article{Thomas-Agnan2013,
-abstract = {We address the question of measuring and testing industrial spatial concentration based on micro-geographic data with distance-based methods. We discuss the basic requirements for such measures and we propose four additional requirements. We also discuss the null assumptions classically used for testing aggregation of a particular sector and propose an alternative point of view. Our general index measure involves a cumulative and a non-cumulative version. This allows us to propose an alternative version of the Duranton–Overman index with a proper baseline as well as a cumulative version of this same index. We present simulations to evaluate the respective powers of this new approach and the classical ones.},
-annote = {MSC 62M30
-19 pages},
-author = {Bonneu, Florent and Thomas-Agnan, Christine},
-doi = {10.1080/17421772.2015.1062124},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonneu, Thomas-Agnan - 2015 - Measuring and testing spatial mass concentration of micro-geographic data.pdf:pdf},
-journal = {Spatial Economic Analysis},
-number = {3},
-pages = {289--316},
-title = {{Measuring and testing spatial mass concentration of micro-geographic data}},
-url = {http://hal.archives-ouvertes.fr/hal-00874201},
-volume = {10},
-year = {2015}
-}
-@article{Pielou1960,
-author = {Pielou, Evelyn C.},
-doi = {10.2307/2257334},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1960 - A single mechanism to account for regular, random and aggregated populations.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {575--584},
-title = {{A single mechanism to account for regular, random and aggregated populations}},
-url = {https://www.jstor.org/stable/2257334},
-volume = {48},
-year = {1960}
-}
-@article{Cadotte2015a,
-abstract = {1. For experiments that link manipulated biodiversity to ecosystem function (EF), phylogenetic diversity (PD) has been an especially powerful form of biodiversity that explains variation in EF. PD represents the total amount of evolutionary history or genetic changes represented by a suite of species and potentially the total accumulation of species niche and functional differences. Analyses often use PD in linear models and assume that ecological differences are proportional to phylogenetic distances. Yet, it is unclear whether alternative models of evolutionary change would improve both the statistical fit and conceptual understanding of how PD influences EF. 2. Here, I use a PD–EF relationship and systematically alter models of evolution including changes in the rate of evolution from phylogenetic root–to-tip and constancy of evolutionary rate across clades. I also compare the PD–EF relationship to several randomization procedures that sequentially remove aspects of the observed phylogeny. 3. I show that changing edge lengths with evolutionary models does not strongly affect PD– EF relationships. Moreover, the observed relationship was not substantially different than the explanation provided by a phylogenetic tree with edge lengths randomized, but was significantly better than randomizations that affected the topology of the phylogenetic trees. 4. These results reveal that changes to the edge lengths have little effect on PD–EF relationships, and it is the topology that really matters. Further, placing species in their correct phylogenetic positions is much more important than developing better estimates of edge lengths.},
-author = {Cadotte, Marc W.},
-doi = {10.1111/1365-2435.12429},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte - 2015 - Phylogenetic diversity-ecosystem function relationships are insensitive to phylogenetic edge lengths.pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {718--723},
-title = {{Phylogenetic diversity-ecosystem function relationships are insensitive to phylogenetic edge lengths}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12429/full},
-volume = {29},
-year = {2015}
-}
-@article{Legendre2001,
-abstract = {This paper examines how to obtain species biplots in unconstrained or constrained ordination without resorting to the Euclidean distance [used in principal component analysis (PCA) and redundancy analysis (RDA)] or the chi-square distance [preserved in correspondence analysis (CA) and canonical correspondence analysis (CCA)] which are not always appropriate for the analysis of community composition data. To achieve this goal, transformations are proposed for species data tables. They allow ecologists to use ordination methods such as PCA and RDA, which are Euclidean-based, for the analysis of community data, while circumventing the problems associated with the Euclidean distance, and avoiding CA and CCA which present problems of their own in some cases. This allows the use of the original (transformed) species data in RDA carried out to test for relationships with explanatory variables (i.e. environmental variables, or factors of a multifactorial analysis- of-variance model); ecologists can then draw biplots displaying the relationships of the species to the explanatory variables. Another application allows the use of species data in other methods of multivariate data analysis which optimize a least-squares loss function; an example is K-means partitioning.},
-author = {Legendre, Pierre and Gallagher, Eugene},
-doi = {10.1007/s004420100716},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Gallagher - 2001 - Ecologically meaningful transformations for ordination of species data.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {271--280},
-title = {{Ecologically meaningful transformations for ordination of species data}},
-url = {http://link.springer.com/10.1007/s004420100716},
-volume = {129},
-year = {2001}
-}
-@article{Sol2017,
-abstract = {Despite the recognised conservation value of phylogenetic diversity, little is known about how it is affected by the urbanisation process. Combining a complete avian phylogeny with surveys along urbanisation gradients from five continents, we show that highly urbanised environments supported on average 450 million fewer years of evolutionary history than the surrounding natural environments. This loss was primarily caused by species loss and could have been higher had not been partially compensated by the addition of urban exploiters and some exotic species. Highly urbanised environments also supported fewer evolutionary distinctive species, implying a disproportionate loss of evolutionary history. Compared with highly urbanised environments, changes in phylogenetic richness and evolutionary distinctiveness were less substantial in moderately urbanised environments. Protecting pristine environments is therefore essential for maintaining phylogenetic diversity, but moderate levels of urbanisation still preserve much of the original diversity.},
-author = {Sol, Daniel and Bartomeus, Ignasi and Gonz{\'{a}}lez-Lagos, C{\'{e}}sar and Pavoine, Sandrine},
-doi = {10.1111/ele.12769},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sol et al. - 2017 - Urbanisation and the loss of phylogenetic diversity in birds.pdf:pdf},
-issn = {14610248},
-journal = {Ecology Letters},
-pages = {721--729},
-title = {{Urbanisation and the loss of phylogenetic diversity in birds}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12769/abstract},
-volume = {20},
-year = {2017}
-}
-@article{Kullback1951,
-author = {Kullback, S. and Leibler, R. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kullback, Leibler - 1951 - On Information and Sufficiency.pdf:pdf},
-journal = {The Annals of Mathematical Statistics},
-number = {1},
-pages = {79--86},
-title = {{On Information and Sufficiency}},
-volume = {22},
-year = {1951}
-}
-@incollection{Boswell1971,
-abstract = {The logarithmic distribution has been studied and applied in the recent past (for references see Patil and Joshi [12], p. 251) to different kinds of situations. N{\~{}}turally one wonders about the underlying chance mechanisms. It turns out that there are several such mechanisms which have no apparent relationship. The emphasis of this paper is on bringing together in a single notation stochastic models generating the logarithmic series distribution (.!2.{\pounds}).r and the basic character of the paper is that of a systematic review and exposition of the available results on the subject. A few new results and comments given at one plaCe or another in the paper will, hopefully, clarify the structure of this important distribution. To preserve the continuity of the discussion, the theorems and their proofs, t.n most of tho cases, are presented in the appendix at the end.},
-author = {Boswell, M. T. and Patil, Ganapati P.},
-booktitle = {Statistical ecology},
-editor = {Patil, Ganapati P. and Pielou, E. C. and Waters, W. E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Boswell, Patil - 1971 - Chance mechanisms generating logarithmic series distribution used in the analysis of number of species and indiv.pdf:pdf},
-pages = {99--130},
-publisher = {Pennsylvania State University Press},
-title = {{Chance mechanisms generating logarithmic series distribution used in the analysis of number of species and individuals}},
-url = {http://sites.psu.edu/gppaddendum/wp-content/uploads/sites/41917/2016/04/8.2-Boswell-M.T.-and-Patil-G.P.-1971.-Chance-mechanisms-generating-logarithmic-series-distribution-used-in-the-analysis-of-number-of-species-and-individuals.-In-Statistical-Ecology-Vo},
-volume = {3},
-year = {1971}
-}
-@article{Shorrocks1980,
-abstract = {An additively decomposable inequality measure is one which can be expressed as a weighted sum of the inequality values calculated for population subgroups plus the contribution arising from differences between subgroup means. The paper derives the entire class of measures which are additively decomposable under relatively weak restric- tions on the form of the index. The subclass of mean independent measures turns out to be a single parameter family which includes the square of the coefficient of variation and two entropy formulae proposed by Theil.},
-author = {Shorrocks, A. F.},
-doi = {10.2307/1913126},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shorrocks - 1980 - The Class of Additively Decomposable Inequality Measures.pdf:pdf},
-issn = {00129682},
-journal = {Econometrica},
-month = {apr},
-number = {3},
-pages = {613},
-title = {{The Class of Additively Decomposable Inequality Measures}},
-url = {http://www.jstor.org/stable/1913126},
-volume = {48},
-year = {1980}
-}
-@article{Pavoine2014b,
-abstract = {1. Ecological studies often rely on coefficients of intercommunity (dis)similarity to decipher effects of ecological, evolutionary and human-drivenmechanisms on the composition of communities.Yet, two main criticisms have been levelled at (dis)similarity coefficients. First, few developments include information on species' abundances, and either phylogeny or functional traits. Secondly, some (dis)similarity coefficients fail to always providemaximum dissimilarity between two completely distinct communities, that is, communities without common species andwith zero similarities among their species. 2. Here,we introduce a new family of similarity coefficients responding to these criticisms. Within this family,we concentrate on four coefficients and compare them to Rao's dissimilarity on macroinvertebrate communities, and simulated data. 3. Our new coefficients correctly treat maximally dissimilar communities: similarities are always zero between two completely distinct communities. The originality of these newcoefficients is evenmore profound as the existence of maximally dissimilar communities was not a requirement for the new coefficients to behave differently than Rao's dissimilarity coefficient. 4. Our new family of similarity coefficients relies on the abundances or occurrences of species within communities and on phylogenetic, taxonomic or functional similarities among species.We demonstrate that this new family embedsmany of the recent developments in both functional and phylogenetic diversity. It provides a unique framework for comparing traditional compositional turnoverwith functional or phylogenetic similaritiesamong communities},
-author = {Pavoine, Sandrine and Ricotta, Carlo},
-doi = {10.1111/2041-210X.12193},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Ricotta - 2014 - Functional and phylogenetic similarity among communities.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {7},
-pages = {666--675},
-title = {{Functional and phylogenetic similarity among communities}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12193},
-volume = {5},
-year = {2014}
-}
-@book{Carnot1824,
-address = {Paris},
-author = {Carnot, Sadi},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carnot - 1824 - R{\'{e}}flexions sur la puissance motrice du feu.pdf:pdf},
-publisher = {Bachelier},
-title = {{R{\'{e}}flexions sur la puissance motrice du feu}},
-year = {1824}
-}
-@article{Shapiro1985a,
-author = {Shapiro, M. B. and Schein, S. J. and de Monasterio, F. M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shapiro, Schein, Monasterio - 1985 - Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina Rejoinder.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-keywords = {Shapiro (1985b).pdf},
-mendeley-tags = {Shapiro (1985b).pdf},
-number = {392},
-pages = {814},
-title = {{Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina: Rejoinder}},
-volume = {80},
-year = {1985}
-}
-@article{Audretsch1998,
-abstract = {A paradox has been the emergence of the importance of local proximity and geographic clusters precisely at a time when globalization seems to dominate economic activity. The purpose of this paper is to resolve this paradox by explaining why and how geography matters for innovative activity and ultimately for the international comparative advantage. Globalization and the telecommunications revolution have triggered a shift in the comparative advantage of the leading developed countries towards an increased importance of innovative activity. This shift in comparative advantage has increased the value of knowledge-based economic activity. Since knowledge is generated and transmitted more efficiently via local proximity, economic activity based on new knowledge has a high propensity to cluster within a geographic region. This has triggered a fundamental shift in public policy towards business, away from policies constraining the freedom of firms to contract and towards a new set of enabling policies, implemented at the regional and local levels.},
-author = {Audretsch, David B.},
-doi = {10.1093/oxrep/14.2.18},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Audretsch - 1998 - Agglomeration and the location of innovative activity.pdf:pdf},
-journal = {Oxford Review of Economic Policy},
-number = {2},
-pages = {18--29},
-title = {{Agglomeration and the location of innovative activity}},
-url = {http://oxrep.oxfordjournals.org/content/14/2/18.short},
-volume = {14},
-year = {1998}
-}
-@article{Korner2000,
-author = {K{\"{o}}rner, Christian},
-doi = {10.1016/S0169-5347(00)02004-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/K{\"{o}}rner - 2000 - Why are there global gradients in species richness Mountains might hold the answer.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {12},
-pages = {513--514},
-title = {{Why are there global gradients in species richness? Mountains might hold the answer}},
-url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(00)02004-8},
-volume = {15},
-year = {2000}
-}
-@article{Morisita1959,
-author = {Morisita, Masaaki},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Morisita - 1959 - Measuring of interspecific association and similarity between communities.pdf:pdf},
-journal = {Memoirs of the Faculty of Science, Kyushu University, Series E (Biology)},
-number = {1},
-pages = {65--80},
-title = {{Measuring of interspecific association and similarity between communities}},
-url = {http://reference.morisita.gr.jp/paper{\_}pdf/56.pdf},
-volume = {3},
-year = {1959}
-}
-@article{Steen1996,
-abstract = {Many species exhibit regional synchrony in population dynamics, and different influential biotic and abiotic factors can be indicated by the observed scale of spatial synchrony. Here, we present analyses of spatial patterns of bank vole Clethrionomys glareolus population fluctuations, based on a 5-yr (1990-1994) trapping series obtained from 31 trap stations regularly spaced along a 256-km transect in the boreal forest in southeastern Norway. The bank vole was known to exhibit typically cyclic population dynamics in this region prior to this study. Bank vole fall densities exhibited fluctuations with little year-to-year variation; all s-indices (a measure of temporal variability) were below 0.5. There was a large scale trend in the temporal variability of the populations, with highest variablity at the south end and lowest in the middle of the transect. Analysis (Mantel correlogram) of the year-to-year rate of change of local populations showed that the opposite ends of the transect appeared to be most out of phase. At a smaller spatial scale (up to 30-40 km), local populations exhibited statistically significant synchrony in growth patterns. Spatiotemporal patterns in the dynamics of local populations were not related to habitat quality. We suggest that the scale domain of population synchrony is related to intrinsic population scaling properties such as dispersal capacity.},
-author = {Steen, Harald and Ims, Rolf A. and Sonerud, Geir A.},
-doi = {10.2307/2265738},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Steen, Ims, Sonerud - 1996 - Spatial and Temporal Patterns of Small-Rodent Population Dynamics at a Regional Scale.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2365--2372},
-title = {{Spatial and Temporal Patterns of Small-Rodent Population Dynamics at a Regional Scale}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/2265738/abstract},
-volume = {77},
-year = {1996}
-}
-@book{Emlen1973,
-author = {Emlen, John Meritt},
-publisher = {Addison-Wesley Publishing Co.},
-title = {{Ecology: an Evolutionary Approach}},
-year = {1973}
-}
-@incollection{Duranton2003,
-author = {Duranton, Gilles and Puga, Diego},
-booktitle = {Handbook of Regional and Urban Economics},
-chapter = {4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton et al. - 2004 - Micro-foundations of urban agglomeration economies.pdf:pdf},
-pages = {2063--2117},
-title = {{Micro-foundations of urban agglomeration economies}},
-year = {2004}
-}
-@article{Call2003,
-abstract = {Invasive exotic plants can persist and successfully spread within ecosystems and negatively affect the recruitment of native species. The exotic invasive Ailanthus altissima and the native Robinia pseudoacacia are frequently found in disturbed sites and exhibit similar growth and reproductive characteristics, yet each has distinct functional roles such as allelopathy and nitrogen fixation, respectively. Spatial point pattern analysis of trees in a silvicultural experiment was used to analyze the potential intraspecific and interspecific interference between these two species by looking at their individual spatial distribution and their spatial association. Analysis of spatial point patterns in the field with Ripley's K indicated that A. altissima and R. pseudoacacia were positively associated with each other along the highly disturbed skid trails in the majority of the field sites. Robinia pseudoacacia was clumped in the majority of the sites, whereas A. altissima was randomly distributed in most sites. Locally, increased disturbances could lead to more opportunities for A. altissima to invade, interact with R pseudoacacia and other native species and potentially have an effect on the native plant community.},
-annote = {Article
-English
-AMER MIDLAND NATURALIST
-698GK},
-author = {Call, L. J. and Nilsen, E. T.},
-doi = {10.1674/0003-0031(2003)150[0001:AOSPAS]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Call, Nilsen - 2003 - Analysis of spatial patterns and spatial association between the invasive tree-of-heaven (Ailanthus altissima) and.pdf:pdf},
-journal = {American Midland Naturalist},
-number = {1},
-pages = {1--14},
-title = {{Analysis of spatial patterns and spatial association between the invasive tree-of-heaven (Ailanthus altissima) and the native black locust (Robinia pseudoacacia)}},
-url = {http://link.springer.com/article/10.1007/s11258-004-0338-0},
-volume = {150},
-year = {2003}
-}
-@article{Stein1991,
-abstract = {A class of edge-corrected estimators for the reduced second moment measure of a stationary isotropic point process is proposed. All estimators in this class have the same unbiasedness properties as previously suggested edge-corrected estimators. One natural element in this class has superior asymptotic properties to existing estimators when the underlying process is Poisson. A simulation study shows that this superiority also holds for certain cluster processes.},
-author = {Stein, Michael L.},
-doi = {10.1093/biomet/78.2.281},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stein - 1991 - A New Class of Estimators for the Reduced Second Moment Measure of Point Processes.pdf:pdf},
-journal = {Biometrika},
-number = {2},
-pages = {281--286},
-title = {{A New Class of Estimators for the Reduced Second Moment Measure of Point Processes}},
-url = {https://doi.org/10.1093/biomet/78.2.281},
-volume = {78},
-year = {1991}
-}
-@article{Stirling2007,
-abstract = {This paper addresses the scope for more integrated general analysis of diversity in science, technology and society. It proposes a framework recognizing three necessary but individually insufficient properties of diversity. Based on 10 quality criteria, it suggests a general quantitative non-parametric diversity heuristic. This allows the systematic exploration of diversity under different perspectives, including divergent conceptions of relevant attributes and contrasting weightings on different diversity properties. It is shown how this heuristic may be used to explore different possible trade-offs between diversity and other aspects of interest, including portfolio interactions. The resulting approach offers a way to be more systematic and transparent in the treatment of scientific and technological diversity in a range of fields, including conservation management, research governance, energy policy and sustainable innovation.},
-author = {Stirling, Andy},
-doi = {10.1098/rsif.2007.0213},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stirling - 2007 - A general framework for analysing diversity in science, technology and society.pdf:pdf},
-journal = {Journal of the Royal Society, Interface},
-number = {15},
-pages = {707--719},
-title = {{A general framework for analysing diversity in science, technology and society}},
-volume = {4},
-year = {2007}
-}
-@article{Hutcheson1970,
-author = {Hutcheson, Kermit},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hutcheson - 1970 - A Test for Comparing Diversities Based on the Shannon Formula.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-pages = {151--154},
-title = {{A Test for Comparing Diversities Based on the Shannon Formula}},
-volume = {29},
-year = {1970}
-}
-@article{Gregorius1978,
-abstract = {To do its broader meaning justice, the most basic characteristics of the general concept of diversity measurement are compiled, and a class of measures complying with the conditions of the concept is presented. Application to the measurement of genetic variation shows that, in particular, the common notion of genic diversity for multiple loci suffers from vagueness. An attempt towards clarification and resolution of the problem is made via redefinition of the elements of the gene pool. It is found that extension of single-locus (allelic) diversities to multiple loci by taking the mean over loci is inadequate. After computing the theoretical bounds for the proportion of heterozygotes given the underlying allelic frequencies within a population, it is concluded that in many cases intra-populational heterozygosity is completely unrelated to genic diversity. On the other hand, in comparing diversities of different populations, two kinds of theoretical inter-populational heterozygosity play a central role in illuminating its relationship to genetic distance between populations. On this occasion, it turns out that one particular measure of genetic distance reflects directly an important minimum property of heterozygosity.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.1016/0025-5564(78)90040-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 1978 - The concept of genetic diversity and its formal relationship to heterozygosity and genetic distance.pdf:pdf},
-journal = {Mathematical Biosciences},
-number = {3-4},
-pages = {253--271},
-title = {{The concept of genetic diversity and its formal relationship to heterozygosity and genetic distance}},
-url = {http://www.sciencedirect.com/science/article/pii/0025556478900408},
-volume = {41},
-year = {1978}
-}
-@article{Reich2004,
-abstract = {A global data set including 5,087 observations of leaf nitrogen (N) and phosphorus (P) for 1,280 plant species at 452 sites and of associated mean climate indices demonstrates broad biogeographic patterns. In general, leaf N and P decline and the N/P ratio increases toward the equator as average temperature and growing season length increase. These patterns are similar for five dominant plant groups, coniferous trees and four angiosperm groups (grasses, herbs, shrubs, and trees). These results support the hypotheses that (i) leaf N and P increase from the tropics to the cooler and drier midlatitudes because of temperature-related plant physiological stoichiometry and biogeographical gradients in soil substrate age and then plateau or decrease at high latitudes because of cold temperature effects on biogeochemistry and (h) the N/P ratio increases with mean temperature and toward the equator, because P is a major limiting nutrient in older tropical soils and N is the major limiting nutrient in younger temperate and high-latitude soils.},
-author = {Reich, Peter B. and Oleksyn, Jacek},
-doi = {10.1073?pnas.0403588101},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reich, Oleksyn - 2004 - Global patterns of plant leaf N and P in relation to temperature and latitude.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {30},
-pages = {11001--11006},
-title = {{Global patterns of plant leaf N and P in relation to temperature and latitude}},
-volume = {101},
-year = {2004}
-}
-@article{Pavoine2004,
-abstract = {This paper presents a new ordination method to compare several communities containing species that differ according to their taxonomic, morphological or biological features. The objective is first to find dissimilarities among communities from the knowledge about differences among their species, and second to describe these dissimilarities with regard to the feature diversity within communities. In 1986, Rao initiated a general framework for analysing the extent of the diversity. He defined a diversity coefficient called quadratic entropy and a dissimilarity coefficient and proposed a decomposition of this diversity coefficient in a way similar to ANOVA. Furthermore, Gower and Legendre (1986) built a weighted principal coordinate analysis. Using the previous context, we propose a new method called the double principal coordinate analysis (DPCoA) to analyse the relation between two kinds of data. The first contains differences among species (dissimilarity matrix); the second the species distribution among communities (abundance or presence/absence matrix). A multidimensional space assembling the species points and the community points is built. The species points define the original differences between species and the community points define the deduced differences between communities. Furthermore, this multidimensional space is linked with the diversity decomposition into between-community and within-community diversities. One looks for axes that provide a graphical ordination of the communities and project the species onto them. An illustration is proposed comparing bird communities which live in different areas under mediterranean bioclimates. Compared to some existing methods, the double principal coordinate analysis can provide a typology of communities taking account of an abundance matrix and can include dissimilarities among species. Finally, we show that such an approach generalizes some of these methods and allows us to developnew analyses.},
-author = {Pavoine, Sandrine and Dufour, Anne-B{\'{e}}atrice and Chessel, Daniel},
-doi = {10.1016/j.jtbi.2004.02.014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Dufour, Chessel - 2004 - From dissimilarities among species to dissimilarities among communities a double principal coordinate.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {4},
-pages = {523--537},
-title = {{From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis}},
-volume = {228},
-year = {2004}
-}
-@article{Pavoine2011a,
-abstract = {P{\textgreater}1. We introduce a novel method that analyses environmental filtering of plant species in a geographic and phylogenetic context. By connecting species traits with phylogeny, traits with environment, and environment with geography, this comprehensive approach partitions the ecological and evolutionary processes that influence community assembly. 2. Our analysis extends RLQ ordination, which connects site attributes in matrix R (here environmental variables and spatial positions) with species attributes in matrix Q (here biological traits and phylogenetic positions), through the composition of sites in terms of species presences or abundances (matrix L). This methodology, which explores and identifies environmental filters that organize communities, was developed to answer four questions: which combinations of trait states are filtered by the environment, which lineages are affected by these filters, which environmental variables contribute to the assemblage of local communities and where do these filters act? 3. At La Mafragh in north-eastern Algeria, our approach shows that plant species traits were distributed according to environmental filters associated with a salinity gradient. Traits associated with the salinity gradient were convergent among Juncaceae, Cyperaceae and Amaranthaceae. The observed phylogenetic and trait patterns were related to how species survived the xeric season. Juncaceae and Cyperaceae, being perennials and anemogamous, tolerate the xeric hot season by restricting their range to the humid centre of the study area (where conditions are close to a subtropical climate). Several Amaranthaceae species co-occur with the Juncaceae and Cyperaceae in two areas with the highest salinity. Most dicots were observed at higher elevations (up to 7 m a.s.l.), had hairy structures that can retain water and reflect solar radiation and were mostly annual or biennial, completing their life cycle before the onset of the xeric season. 4. Synthesis. Our methodology describes environmental filters in terms of identified combinations of traits and environmental factors. It allows spatial and phylogenetic signals to be determined by identifying convergent and conserved patterns in the evolution of traits and spatial scales that structured the environment. Our statistical framework is generic and can be readily extended to a wide range of exciting issues, such as host-parasite, plant-pollinator and predator-prey interactions.},
-annote = {ISI Document Delivery No.: 694MA
-Times Cited: 22
-Cited Reference Count: 77
-Pavoine, Sandrine Vela, Errol Gachet, Sophie de Belair, Gerard Bonsall, Michael B.
-European Commission; Royal Society
-We thank the referees and the editor for their constructive comments. We are also grateful to Stephane Dray for useful discussion on the fourth-corner approach. The work was supported by the European Commission under the Marie Curie Programme (S.P.) and the Royal Society (M.B.B.).
-Wiley-blackwell
-Hoboken},
-author = {Pavoine, Sandrine and Vela, Errol and Gachet, Sophie and de Belair, G{\'{e}}rard and Bonsall, Michael B.},
-doi = {10.1111/j.1365-2745.2010.01743.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2011 - Linking patterns in phylogeny, traits, abiotic variables and space a novel approach to linking environmental fil.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {165--175},
-title = {{Linking patterns in phylogeny, traits, abiotic variables and space: a novel approach to linking environmental filtering and plant community assembly}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2010.01743.x/abstract},
-volume = {99},
-year = {2011}
-}
-@article{Qian2005,
-abstract = {The diversity of a region reflects both local diversity and the turnover of species (beta diversity) between areas. The angiosperm flora of eastern Asia (EAS) is roughly twice as rich as that of eastern North America (ENA), in spite of similar area and climate. Using province/state-level angiosperm species floras, we calculated beta diversity as the slope of the relationship between the log of species similarity (S ) and either geographic distance or difference in climate. Distance-based beta diversity was 2.6 times greater in the north-south direction in EAS than in ENA and 3.3 times greater in the east-west direction. When ln S was related to distance and climate difference in multiple regressions, both distance and climate PC1 were significant effects in the north-south direction, but only geographic distance had a significant, unique influence in the east-west direction. The general predominance of distance over environment in beta diversity suggests that history and geography have had a strong influence on the regional diversity of these temperate floras.},
-annote = {ISI Document Delivery No.: 879WQ
-Times Cited: 50
-Cited Reference Count: 40
-BLACKWELL PUBLISHING LTD},
-author = {Qian, H. and Ricklefs, Robert E. and White, Peter S.},
-doi = {10.1111/j.1461-0248.2004.00682.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Qian, Ricklefs, White - 2005 - Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America.pdf:pdf},
-journal = {Ecology Letters},
-number = {1},
-pages = {15--22},
-title = {{Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America}},
-volume = {8},
-year = {2005}
-}
-@article{Chiu2016,
-abstract = {Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures' emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes.},
-author = {Chiu, Chun-Huo and Chao, Anne},
-doi = {10.7717/peerj.1634},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu, Chao - 2016 - Estimating and comparing microbial diversity in the presence of sequencing errors.pdf:pdf},
-journal = {PeerJ},
-pages = {e1634},
-title = {{Estimating and comparing microbial diversity in the presence of sequencing errors}},
-volume = {4},
-year = {2016}
-}
-@article{Chao2016b,
-abstract = {Species richness (the number of species) in an assemblage is a key metric in many research fields of ecology. Simple counts of species in samples typically underestimate the true species richness and strongly depend on sampling effort and sample completeness. Based on possibly unequal-sampling effort and incomplete samples that miss many species, there are two approaches to infer species richness and make fair comparisons among multiple assemblages,: (1) An asymptotic approach via species richness estimation. This approach aims to compare species richness estimates across assemblages. We focus on the nonparametric estimators that are universally valid for all species abundance distributions. (2) A non-asymptotic approach via the sample-size- and coverage-based rarefaction and extrapolation on the basis of standardised sample size or sample completeness (as measured by sample coverage). This approach aims to compare species richness estimates for equally large or equally complete samples. Two R packages (SpadeR and iNEXT) are applied to beetle data for illustration.},
-author = {Chao, Anne and Chiu, Chun-Huo},
-doi = {10.1002/9780470015902.a0026329},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu - 2016 - Nonparametric Estimation and Comparison of Species Richness.pdf:pdf},
-journal = {eLS},
-title = {{Nonparametric Estimation and Comparison of Species Richness}},
-url = {http://doi.wiley.com/10.1002/9780470015902.a0026329},
-volume = {in press},
-year = {2016}
-}
-@article{Wang2013,
-abstract = {Phylogenetic diversity (PD, the diversity of lineages) and functional diversity (FD, the diversity of functional traits or groups in a biological community) reflect important yet poorly understood attributes of species assemblages. Until recently, few studies have examined the spatial variation of PD and FD in natural communities. Yet the relationships between PD and FD and area (termed PDAR and FDAR), like the analogous species–area relationship (SAR), have received less attention and may provide insights into the mechanisms that shape the composition and dynamics of ecological communities. In this study, we used four spatial point process models to evaluate the likely roles of the random placement of species, habitat filtering, dispersal limitation, and the combined effects of habitat filtering and dispersal limitation in producing observed PDARs and FDARs in two large, fully mapped temperate forest research plots in northeast China and in north-central USA. We found that the dispersal limitation hypothesis provided a good approximation of the accumulation of PD and FD with increasing area, as it did for the species area curves. PDAR and FDAR patterns were highly correlated with the SAR. We interpret this as evidence that species interactions, which are often influenced by phylogenetic and functional similarity, may be relatively unimportant in structuring temperate forest tree assemblages at this scale. However, the scale-dependent departures of the PDAR and FDAR that emerged for the dispersal limitation hypothesis agree with operation of competitive exclusion at small scales and habitat filtering at larger scales. Our analysis illustrates how emergent community patterns in fully mapped temperate forest plots can be influenced by multiple underlying processes at different spatial scales.},
-author = {Wang, Xugao and Swenson, Nathan G. and Wiegand, Thorsten and Wolf, Amy and Howe, Robert and Lin, Fei and Ye, Ji and Yuan, Zuoqiang and Shi, Shuai and Bai, Xuejiao and Xing, Dingliang and Hao, Zhanqing},
-doi = {10.1111/j.1600-0587.2012.00011.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wang et al. - 2013 - Phylogenetic and functional diversity area relationships in two temperate forests.pdf:pdf},
-journal = {Ecography},
-number = {8},
-pages = {883--893},
-title = {{Phylogenetic and functional diversity area relationships in two temperate forests}},
-url = {http://dx.doi.org/10.1111/j.1600-0587.2012.00011.x},
-volume = {36},
-year = {2013}
-}
-@book{Kohl2016,
-abstract = {This book provides a cross-section of all outstanding experience in all fields of tropical forestry under a drastically changing environment induced by climate change. It sheds light on the existing know-how and presents it in a concise and efficient way for the scientist and professional in charge of planning, implementing and evaluating forest resources. The Tropical Forestry Handbook provides proven and/or promising alternative concepts which can be applied to solve organizational, administrative and technical challenges prevailing in the tropics. Presented are state of the art methods in all fields concerning tropical forestry. Emphasis is given to methods which are adapted to- and which safeguard - environmental conditions.},
-editor = {Pancel, Laslo and K{\"{o}}hl, Michael},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pancer-Koteja, Szwagrzyk, Bodziarczyk - 1998 - Small-scale spatial pattern and size structure of Rubus hirtus in a canopy gap.pdf:pdf},
-isbn = {9783642546006},
-title = {{Tropical Forestry Handbook}},
-year = {2016}
-}
-@article{Podani2013,
-abstract = {We describe a procedure for evaluating the relative importance of beta diversity, nestedness, and similarity properties of ecological data matrices containing density, cover or biomass scores of species. Our goals are achieved by extension of the simplex approach – originally proposed for presence–absence data – to abundances. Basically, the method involves decomposition of the Marczewski–Steinhaus coefficient of dissimilarity between pairs of sites into two fractions, one derived from differences between total abundance and the other from differences due to abundance replacement. These are contrasted by the similarity function counterpart, known as the Ruzicka coefficient, and are displayed graphically using ternary (or 2D simplex) plots. Interpretation is aided by calculating percentage contributions from these components to the (dis)similarity structure. Measures of replacement and nestedness are new for abundance data; these are considered complementary phenomena reflecting antithetic ecological processes that are analogous to those operating at the presence–absence level. The method is illustrated by artificial data and a range of actual ecological data sets representing different groups of organisms, different scales and different types of data. While the simplex diagrams and associated coefficients are meaningful by themselves, their comparison with presence–absence based results gives additional insight into data structure and background factors.},
-annote = {From Duplicate 2 ( A general framework for analyzing beta diversity, nestedness and related community-level phenomena based on abundance data - Podani, J; Ricotta, C; Schmera, D )
-
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Podani, J.; Department of Plant Systematics, Ecology and Theoretical Biology and Ecology Research Group of HAS, Institute of Biology, L. E{\"{o}}tv{\"{o}}s University, P{\'{a}}zm{\'{a}}ny P. s. 1/C, H-1117 Budapest, Hungary; email: podani@ludens.elte.hu},
-author = {Podani, J{\'{a}}nos and Ricotta, Carlo and Schmera, D{\'{e}}nes},
-doi = {10.1016/j.ecocom.2013.03.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani, Ricotta, Schmera - 2013 - A general framework for analyzing beta diversity, nestedness and related community-level phenomena bas.pdf:pdf},
-journal = {Ecological Complexity},
-pages = {52--61},
-title = {{A general framework for analyzing beta diversity, nestedness and related community-level phenomena based on abundance data}},
-url = {http://www.sciencedirect.com/science/article/pii/S1476945X13000329},
-volume = {15},
-year = {2013}
-}
-@inproceedings{Pelissier2014,
-abstract = {Spatial pattern of ecological diversity may result from the combine effects of various ecological processes: species migration/colinisation, dispersal of propagules, inter-individual competition/facilitation, habitat preferences, etc. While powerful methods exist for quantifying species diversity on the one hand and spatial patterns on the other hand, current methods do not take full advantage of an integrative approach that could improve robustness of inferences about ecological processes at the origin of observed patterns. We propose here such an integration based on Rao quadratic entropy for a flexible quantification of species diversity accounting for non-uniform between species differences (such as phylogenetic or functional differences) and well established methods of spatial pattern analysis. For the case of fully mapped data (for instance, trees beyond a given threshold in an exhaustively sampled forest plot), a distance-dependent quantification of the spatial variation in alpha diversity is obtained by combining Rao quadratic entropy with Ripley's K-function of second-order neighbourhood analysis. For the case of discontinuous spatial samples (for instance, a network of independent forest plots), a distance-dependent quantification of the spatial variation in beta-diversity results from integration of Rao quadratic entropy within the framework of the variogramms. Beyond methodological consistency for quantifying spatial patterns of species diversity, this integration also allows the development of statistical tests of meaningful ecological mechanisms based on reference null hypotheses about either the spatial arrangement of individuals/samples, or the between-species relatedness as introduced in Rao quadratic entropy. Illustrations are provided based on simulated patterns as well as on observed patterns from tropical forest data.},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l and Couteron, Pierre and Hardy, Olivier and Marcon, Eric and Pavoine, Sandrine},
-booktitle = {International Statistical Ecology Conference},
-pages = {223--224},
-title = {{Quantifying spatial patterns of species diversity: integrating methods of spatial and diversity analyses}},
-url = {https://isec2014.sciencesconf.org/data/pages/Book{\_}of{\_}Abstracts{\_}ISEC2014{\_}Montpellier.pdf},
-year = {2014}
-}
-@book{Baddeley2005a,
-abstract = {We describe practical techniques for fitting stochastic models to spatial point pattern data in the statistical package R. The techniques have been implemented in our package spatstat in R. They are demonstrated on two example datasets.},
-booktitle = {Case studies in spatial point process modeling},
-doi = {10.1007/0-387-31144-0},
-editor = {Baddeley, Adrian and Gregori, Pablo and Mateu, Jorge and Stoica, Radu and Stoyan, Dietrich},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Unknown - 2005 - Case Studies in Spatial Point Process Modeling.pdf:pdf},
-publisher = {Springer},
-title = {{Case Studies in Spatial Point Process Modeling}},
-url = {http://www.amazon.com/dp/0387283110},
-year = {2005}
-}
-@article{Witting1995,
-abstract = {Biodiversity conservat{\&}n {\&} confronted with two major problems." how to define and measure biodiversity, and how to optimize the in situ conservation of biodiversity. Here we outline a conceptual framework for biodiversity conservation that is directed towards these problems. The framework combines a phylogenetic evaluation with a multi-species risk analysis and defines the objective of conservation biology as the minimization of the future loss of biodiversity.},
-author = {Witting, Lars and Loeschcke, Volker},
-doi = {10.1016/0006-3207(94)00041-N},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Witting, Loeschcke - 1995 - The optimization of biodiversity conservation.pdf:pdf},
-journal = {Biological Conservation},
-number = {2},
-pages = {205--207},
-title = {{The optimization of biodiversity conservation}},
-url = {http://www.sciencedirect.com/science/article/pii/000632079400041N},
-volume = {71},
-year = {1995}
-}
-@article{Kempton1979,
-author = {Kempton, R. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kempton - 1979 - The Structure of Species Abundance and Measurement of Diversity.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {307--321},
-title = {{The Structure of Species Abundance and Measurement of Diversity}},
-volume = {35},
-year = {1979}
-}
-@article{Deurloo2008,
-abstract = {A wide variety of segregation measures are used in scientific research. However, the usual measures are not suitable for use at micro-geographical scale level, for example, to evaluate the magnitude of spatial attraction or separation between pairs of ethnic groups within multi-ethnic residential neighbourhoods in Amsterdam. In this paper we examine the social importance of possessing such knowledge for these areas, we discuss the deficiencies of the usual segregation measures as regards this level of analysis, and we draw attention to a recently developed spatial segregation measure, the so-called M measure, which does happen to be suitable for this goal. We apply the M measure to some of these residential neighbourhoods which existed in Amsterdam on 1 January 2003. The conclusion is that although neighbourhoods can have a very similar ethnic mix, the spatial attraction or avoidance between certain pairs of groups may be quite different between these neighbourhoods.},
-author = {Deurloo, Marinus C. and {De Vos}, Sjoerd},
-doi = {10.1111/j.1467-9663.2008.00465.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Deurloo, De Vos - 2008 - Measuring segregation at the micro level an application of the M measure to multi-ethnic residential neighbourh.pdf:pdf},
-journal = {Tijdschrift voor economische en sociale geografie},
-number = {3},
-pages = {329--347},
-title = {{Measuring segregation at the micro level: an application of the M measure to multi-ethnic residential neighbourhoods in Amsterdam}},
-url = {http://dx.doi.org/10.1111/j.1467-9663.2008.00465.x},
-volume = {99},
-year = {2008}
-}
-@article{Brubaker1980,
-abstract = {Regional patterns of ring width anomalies in Washington, Oregon, and Idaho, USA forests are exarnined using eigenvector (principal component) techniques. The first two eigenvectors, accounting for nearly 50{\%} of the total variance, represent large-scale spatial patterns. Eigenvector I represents a pattern in which growth anomalies are positively correlated among all sites, and Eigenvector II one in which growth anomalies are negatively correlated between sites located on opposite sides of the Cascade Mountain crest. These patterns most likely result from two types of tree growth responses to climate variations that extend uniformly across the study area. Common responses to spring-summer rainfall probably cause the positive, region-wide correlations identified by Eigenvector I, and opposite east-West responses to summer temperature and winter precipitation may account for the negative correlations identified by Eigenvector II . No evidence supports the idea that the tree growth eigenvectors directly reflect two distinctive patterns of climate anomalies. The spatial patterns of these tree growth anomalies have remained essentially constant during the past 300 (possibly 400) yr.},
-author = {Brubaker, Linda B.},
-doi = {10.2307/1936750},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brubaker - 1980 - Spatial Patterns of Tree Growth Anomalies in the Pacific Northwest.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {798--807},
-title = {{Spatial Patterns of Tree Growth Anomalies in the Pacific Northwest}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1936750/full},
-volume = {61},
-year = {1980}
-}
-@article{Cole1999,
-abstract = {1 Spatial analysis techniques were used to differentiate between climate-induced and pathogen-induced mass mortalities of the kelp Eckloizia radiata in north-eastern New Zealand. We predicted that climate-induced effects would generate broad-scale patterns, whereas pathogen-induced inortality would be traceable among neighbouring thalli. 2 Spatial autocorrelation analysis was performed on the proportion of E. radiata affected by dieback in quadrats during an initial mortality event in 1991. The absence of any consistent spatial scale of affected thalli between 10 and 100m suggested that small-scale spread of an agent might be occurring. 3 Individual thalli were therefore mapped at two sites during a subsequent mortality event in 1992/93, and the degree of damage recorded. Spatial analyses found little evidence of aggregation of either intact or affected thalli at scales of 1-150 cm. 4 The relative spatial patterns of healthy and affected plants in mapped quadrats during the 1992/93 mortality provided little evidence of spatial association or repulsion between these broad damage categories. 5 The large-scale mortality of 1992/93 was consistent with a physiological response to broad-scale light deprivation, although other agents, perhaps both a virus and amphipod grazing, might also have been involved. Potentially complex interactions among the candidate agents render interpretation of the spatial patterns difficult.},
-author = {Cole, Russell G. and Syms, Craig},
-doi = {10.1046/j.1365-2745.1999.00418.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cole, Syms - 1999 - Using spatial patterns analysis to distinguish causes of mortality an example from kelp in north-eastern New Zealand.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {963--972},
-title = {{Using spatial patterns analysis to distinguish causes of mortality: an example from kelp in north-eastern New Zealand}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2745.1999.00418.x/abstract},
-volume = {87},
-year = {1999}
-}
-@article{Izsak2000,
-abstract = {The practice of environmental planning and protection frequently necessitates the quantification of ecological diversity. Traditional ‘ecological diversity indices' are based on the abundances of species present. However, such indices are insensitive to taxonomic or similar differences. With equal species abundances they measure the species richness (species number) only. Conversely, so-called ‘biodiversity indices' are based on species differences, but are insensitive to the abundance conditions. The quadratic entropy index is the only ecological diversity index, the value of which reflects both the differences ‘and' abundances of the species. When a species list is given without abundance data, then, using the quadratic entropy index and postulating equal abundances, one gets the only biodiversity index derived from a traditional ecological index of diversity. Its extensive form is identical with the sum of differences or distances between the species present. This index trivially satisfies set monotonicity, an important property for biodiversity indices.},
-author = {Izs{\'{a}}k, J{\'{a}}nos and Papp, L.},
-doi = {10.1016/S0304-3800(00)00203-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Izs{\'{a}}k, Papp - 2000 - A link between ecological diversity indices and measures of biodiversity.pdf:pdf},
-journal = {Ecological Modelling},
-pages = {151--156},
-title = {{A link between ecological diversity indices and measures of biodiversity}},
-url = {http://www.sciencedirect.com/science/article/pii/S0304380000002039},
-volume = {130},
-year = {2000}
-}
-@article{Daniel2003a,
-abstract = {L'objet de cet article est d'appr{\'{e}}cier l'{\'{e}}volution de la localisation des productions agricoles dans l'Union europ{\'{e}}enne et de d{\'{e}}terminer si les co{\^{u}}ts de production agricoles et la localisation des bassins de production par rapport {\`{a}} celle des consommateurs europ{\'{e}}ens sont d{\'{e}}terminants de la concentration g{\'{e}}ographique de l'agriculture. L'analyse empirique tend {\`{a}} montrer que la production agricole se concentre g{\'{e}}ographiquement dans les bassins de production les mieux situ{\'{e}}s en termes d'acc{\`{e}}s au march{\'{e}} communautaire.},
-author = {Daniel, Karine},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Daniel - 2003 - Concentration et sp{\'{e}}cialisation quel sch{\'{e}}ma pour l'agriculture communautaire.pdf:pdf},
-journal = {Economie et Pr{\'{e}}vision},
-number = {158},
-pages = {105--120},
-title = {{Concentration et sp{\'{e}}cialisation : quel sch{\'{e}}ma pour l'agriculture communautaire}},
-url = {https://www.cairn.info/revue-economie-et-prevision-2003-2-page-105.htm},
-volume = {2},
-year = {2003}
-}
-@book{Combes2008,
-address = {Princeton, New Jersey},
-author = {Combes, Pierre-Philippe and Mayer, Thierry and Thisse, Jacques-Fran{\c{c}}ois},
-booktitle = {The Integration of Regions and Nations},
-isbn = {978-0691124599},
-pages = {1--416},
-publisher = {Princeton University Press},
-title = {{Economic Geography}},
-year = {2008}
-}
-@article{Jurasinski2009,
-abstract = {Almost half a century after Whittaker (Ecol Monogr 30:279-338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative--depending on the organism(s) or ecosystems investigated--this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term "inventory diversity." Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness ("key concept" vs. "abstruse concept"). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, "differentiation diversity" (first group) and "proportional diversity" (second group). Thus, we propose to use the terms "inventory diversity" for within-sample diversity, "differentiation diversity" for compositional similarity between samples, and "proportional diversity" for the comparison of inventory diversity across spatial and temporal scales.},
-annote = {ISI Document Delivery No.: 396FD
-Times Cited: 8
-Cited Reference Count: 116
-Jurasinski, Gerald Retzer, Vroni Beierkuhnlein, Carl
-SPRINGER},
-author = {Jurasinski, Gerald and Retzer, Vroni and Beierkuhnlein, Carl},
-doi = {10.1007/s00442-008-1190-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jurasinski, Retzer, Beierkuhnlein - 2009 - Inventory, differentiation, and proportional diversity a consistent terminology for quantifyi.pdf:pdf},
-journal = {Oecologia},
-number = {1},
-pages = {15--26},
-title = {{Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs00442-008-1190-z},
-volume = {159},
-year = {2009}
-}
-@article{Terborgh1973,
-abstract = {For many years plant ecologists have espoused the notion that habitats$\backslash$ndiffer in an intrinsic quality that has been called favorableness.$\backslash$nHere I point out that the concept of favorableness is circular and$\backslash$ncounterproductive. I develop the thesis that species diversity is$\backslash$ndetermined by the balance of several dynamic processes: speciation,$\backslash$ncompetition, immigration, adaptation, and extinction. A simple kinetic$\backslash$nmodel places each of these processes in a definite perspective. My$\backslash$narguments are based on the observation that widespread mesic environments$\backslash$ncommonly support vegetation containing greater species diversity$\backslash$nthan environments of more unusual character such as sand dunes, inundated$\backslash$ndepressions, bogs, mountain tops, saline soils, etc. Habitats such$\backslash$nas these, that incorporate uncommon features and are often patchy$\backslash$nand of small total area, are called peripheral habitats. Empirical$\backslash$nand theoretical considerations both lead to the opinion that the$\backslash$npressure of competition in the species-rich communities of mesic$\backslash$nhabitats impels an adaptive outflow of species down gradient toward$\backslash$nrelatively impoverished peripheral habitats. Evolutionary difficulties$\backslash$ninvolved in adapting up a competition gradient argue that the species$\backslash$nflow from core to peripheral habitats is virtually unidirectional.$\backslash$nApplication of the kinetic model to some elementary features of the$\backslash$nearth's geography provides a quantitative result that predicts a$\backslash$nlarge and universal tropical-temperate diversity gradient. The mechanism$\backslash$nis founded on an area-dependent model of speciation coupled to the$\backslash$nestimated rate of environmental change with latitude. It requires$\backslash$nno assumptions about stability, food webs, or niche packing. The$\backslash$nlast section addresses the problem of how the dimensions of plant$\backslash$nniche space could vary between different vegetation formations and$\backslash$nbriefly discusses components of rainforest diversity.},
-author = {Terborgh, John},
-doi = {10.1086/282852},
-isbn = {00030147},
-issn = {0003-0147},
-journal = {American Naturalist},
-number = {956},
-pages = {481--501},
-title = {{On the notion of favorableness in plant ecology}},
-volume = {107},
-year = {1973}
-}
-@book{Shannon1963,
-author = {Shannon, Claude E and Weaver, Warren},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shannon, Weaver - 1963 - The Mathematical Theory of Communication.pdf:pdf},
-isbn = {0252725484},
-publisher = {University of Illinois Press},
-title = {{The Mathematical Theory of Communication}},
-year = {1963}
-}
-@article{MacArthur1957,
-annote = {ArticleType: research-article / Full publication date: Mar. 15, 1957 / Copyright {\^{A}}{\textcopyright} 1957 National Academy of Sciences},
-author = {MacArthur, Robert H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacArthur - 1957 - On the Relative Abundance of Bird Species.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {3},
-pages = {293--295},
-title = {{On the Relative Abundance of Bird Species}},
-url = {http://www.jstor.org/stable/89566},
-volume = {43},
-year = {1957}
-}
-@book{Openshaw1984,
-abstract = {The usefulness of many forms of spatial study, quantitative or other- wise, depends on the nature and intrinsic meaningfulness of the objects that are under study. Geographers have a long tradition of studying data for areal units; for example, spatial objects such as zones or places or towns or regions. The problem is that ever since the demise of 'the region' as the primary object of geographical study very little concern has been ex- pressed about the nature and definition of the spatial objects under study. As Chapman (1977) put it 'Geography has consistently and dismally failed to tackle its entitation problems, and in that more than anything else lies the root of so many of its problems' (page 7). In short insufficient thought is given to precisely what it is that is being studied.},
-address = {Norwich},
-author = {Openshaw, Stan},
-booktitle = {Concepts and Techniques in Modern Geography},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Openshaw - 1984 - The modifiable area unit problem.pdf:pdf},
-isbn = {0860941345},
-issn = {0306-6142},
-publisher = {Geo Books},
-title = {{The modifiable area unit problem}},
-url = {http://qmrg.org.uk/files/2008/11/38-maup-openshaw.pdf},
-volume = {38},
-year = {1984}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2006,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n°2006-781 du 3 juillet 2006 fixant les conditions et les modalit{\'{e}}s de r{\`{e}}glement des frais occasionn{\'{e}}s par les d{\'{e}}placements temporaires des personnels civils de l'Etat}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000242359},
-year = {2006}
-}
-@article{Allard2001,
-abstract = {Dependencies between two types of points in a spatial point process can be due either to a real dependence between the two types or to the dependence on common underlying variables. We propose a global test for dependence between two point processes that is valid for a wide range of models. In contrast with previously proposed methods, it is based on a number of local test statistics, which makes it possible to map the local association between the two processes. The behavior of the test is evaluated by a simulation study. It is then applied to a vegetation pattern data set from Burkina Faso},
-author = {Allard, Denis and Brix, Anders and Chadoeuf, Jo{\"{e}}l},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Allard, Brix, Chadoeuf - 2001 - Testing local independence between two point processes.pdf:pdf},
-journal = {Biometrics},
-number = {2},
-pages = {508--517},
-title = {{Testing local independence between two point processes}},
-volume = {57},
-year = {2001}
-}
-@article{Phillips1981,
-abstract = {(1) Spacing patterns of shrubs were studied on a series of sites in the Mojave and Sonoran Deserts. Both aggregation and regularity in dispersion of individual shrubs were fairly common. Aggregation may result from vegetative reproduction or environmental heterogeneity, and regularity from competition among plants. (2) Small shrubs tend to be clumped, medium-sized ones tend to a random arrangement, and large shrubs tend to a regular pattern. This suggests the increasing importance of competition as the plants grow. (3) Further evidence of interference between plants was provided by the correlations of plant size with the distance to their neighbours. (4) Root systems were extensive enough to abut or overlap each other in the interplant spaces. (5) Most plants tended to have neighbours of the same species rather than other species. (6) None of these results depended on position along the considerable climatic gradients across the Mojave and Sonoran Deserts.},
-author = {Phillips, Donald L and MacMahon, James A},
-doi = {10.2307/2259818},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Phillips, MacMahon - 1981 - Competition and spacing patterns in desert shrubs.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {97--115},
-title = {{Competition and spacing patterns in desert shrubs}},
-url = {http://www.jstor.org/stable/2259818},
-volume = {69},
-year = {1981}
-}
-@article{Weikard2006,
-abstract = {We discuss a diversity measure combining information of relative abundances and taxonomic distinctiveness suggested by Ricotta (2004). We show that Ricotta's measure violates weak species monotonicity, a condition that requires that the addition of a species should always increase a diversity index if abundances change only marginally. We suggest an alternative index satisfying weak species monotonicity and apply it to the 'Zeesserveld' forest reserve in the Netherlands.},
-author = {Weikard, Hans-Peter and Punt, Maarten and Wesseler, Justus},
-doi = {10.1111/j.1366-9516.2006.00234.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weikard, Punt, Wesseler - 2006 - Diversity measurement combining relative abundances and taxonomic distinctiveness of species.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {2},
-pages = {215--217},
-title = {{Diversity measurement combining relative abundances and taxonomic distinctiveness of species}},
-url = {http://dx.doi.org/10.1111/j.1366-9516.2006.00234.x},
-volume = {12},
-year = {2006}
-}
-@article{McCann2000,
-abstract = {There exists little doubt that the Earth's biodiversity is declining. The Nature Conservancy, for example, has documented that one-third of the plant and animal species in the United States are now at risk of extinction. The problem is a monumental one, and forces us to consider in depth how we expect ecosystems, which ultimately are our life-support systems, to respond to reductions in diversity. This issue — commonly referred to as the diversity–stability debate — is the subject of this review, which synthesizes historical ideas with recent advances. Both theory and empirical evidence agree that we should expect declines in diversity to accelerate the simplification of ecological communities.},
-author = {McCann, Kevin Shear},
-doi = {10.1038/35012234},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McCann - 2000 - The diversity-stability debate.pdf:pdf},
-journal = {Nature},
-pages = {228--233},
-title = {{The diversity-stability debate.}},
-url = {http://www.nature.com/nature/journal/v405/n6783/full/405228a0.html},
-volume = {405},
-year = {2000}
-}
-@article{Ripley1978,
-abstract = {The use of the few smallest distances between pairs of points in a spatial pattern for a test of interaction between the points is investigated.},
-author = {Ripley, Brian D. and Silverman, B. W.},
-doi = {10.1093/biomet/65.3.641},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley, Silverman - 1978 - Quick Tests for Spatial Interaction.pdf:pdf},
-journal = {Biometrika},
-number = {3},
-pages = {641--642},
-title = {{Quick Tests for Spatial Interaction}},
-url = {https://doi.org/10.1093/biomet/65.3.641},
-volume = {65},
-year = {1978}
-}
-@article{Violle2007,
-abstract = {In its simplest definition, a trait is a surrogate of organismal performance, and this meaning of the term has been used by evolutionists for a long time. Over the last three decades, developments in community and ecosystem ecology have forced the concept of trait beyond these original boundaries, and trait-based approaches are now widely used in studies ranging from the level of organisms to that of ecosystems. Despite some attempts to fix the terminology, especially in plant ecology, there is currently a high degree of confusion in the use, not only of the term ‘‘trait'' itself, but also in the underlying concepts it refers to. We therefore give an unambiguous definition of plant trait, with a particular emphasis on functional trait. A hierarchical perspective is proposed, extending the ‘‘performance paradigm'' to plant ecology. ‘‘Functional traits'' are defined as morpho-physio- phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival, the three components of individual performance. We finally present an integrative framework explaining how changes in trait values due to environmental variations are translated into organismal performance, and how these changes may influence processes at higher organizational levels. We argue that this can be achieved by developing ‘‘integration functions'' which can be grouped into functional response (community level) and effect (ecosystem level) algorithms.},
-author = {Violle, Cyrille and Navas, Marie-Laure and Vile, Denis and Kazakou, Elena and Fortunel, Claire and Hummel, Ir{\`{e}}ne and Garnier, Eric},
-doi = {10.1111/j.0030-1299.2007.15559.x},
-file = {::},
-journal = {Oikos},
-number = {5},
-pages = {882--892},
-title = {{Let the concept of trait be functional!}},
-url = {http://doi.wiley.com/10.1111/j.0030-1299.2007.15559.x},
-volume = {116},
-year = {2007}
-}
-@article{Routledge1983,
-author = {Routledge, R. D.},
-doi = {10.2307/3544211},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Routledge - 1983 - Evenness indices Are any admissible.pdf:pdf},
-issn = {00301299},
-journal = {Oikos},
-number = {1},
-pages = {149--151},
-title = {{Evenness indices: Are any admissible?}},
-url = {http://www.jstor.org/stable/3544211},
-volume = {40},
-year = {1983}
-}
-@article{Juhasz-Nagy1983,
-abstract = {The use of mathematical methods based on Shannon's entropy function is proposed for the evaluation of the consequences of sampling unit size and for the study of vegetation succession. The concept of diversity is extended to sets of phytosociological relev{\'{e}}s under the term florula diversity. It is shown that Shannon's entropy as well as two other related characteristic functions can express the local behaviour and overall relationships of species. Characteristic areas are defined in terms of the maxima and minima of these functions. Several study areas yielded the data which are used in the examples. Some theoretical problems of the methods are discussed and a computer, written in FORTRAN, is described. {\^{A}}{\textcopyright} 1983 Dr. W. Junk Publishers.},
-annote = {Cited By (since 1996): 36
-Export Date: 28 December 2011
-Source: Scopus
-CODEN: VGTOA
-doi: 10.1007/BF00129432
-Language of Original Document: English
-Correspondence Address: Juh{\~{A}}¡sz-Nagy, P.; Department of Plant Taxonomy and Ecology, L. E{\~{A}}{\P}tv{\~{A}}{\P}s University, M{\~{A}}{\textordmasculine}zeum krt. 4/a, Budapest, H-1088, Hungary},
-author = {Juh{\'{a}}sz-Nagy, P. and Podani, J{\'{a}}nos},
-doi = {10.1007/BF00129432},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Juh{\'{a}}sz-Nagy, Podani - 1983 - Information theory methods for the study of spatial processes and succession.pdf:pdf},
-journal = {Vegetatio},
-number = {3},
-pages = {129--140},
-title = {{Information theory methods for the study of spatial processes and succession}},
-url = {http://link.springer.com/article/10.1007/BF00129432},
-volume = {51},
-year = {1983}
-}
-@article{Lopez2012,
-abstract = {Estimate the richness of a community with accuracy despite differences in sampling effort is a key aspect to monitoring high diverse ecosystems. We compiled a worldwide multitaxa database, comprising 185 communities, in order to study the relationship between the percentage of species represented by one individual (singletons) and the intensity of sampling (number of individuals divided by the number of species sampled). The database was used to empirically adjust a correction factor to improve the performance of non-parametrical estimators under conditions of low sampling effort. The correction factor was tested on seven estimators (Chao1, Chao2, Jack1, Jack2, ACE, ICE and Bootstrap). The correction factor was able to reduce the bias of all estimators tested under conditions of undersampling, while converging to the original uncorrected values at higher intensities. Our findings led us to recommend the threshold of 20 individuals/species, or less than 21{\%} of singletons, as a minimum sampling effort to produce reliable richness estimates of high diverse ecosystems using corrected non-parametric estimators. This threshold rise for 50 individuals/species if non-corrected estimators are used which implies in an economy of 60{\%} of sampling effort if the correction factor is used.},
-author = {Lopez, Luiz Carlos Serramo and {De Aguiar Fracasso}, Maria Paula and Mesquita, Daniel Oliveira and Palma, Alexandre Ramlo Torre and Riul, Pablo},
-doi = {10.1016/j.ecolind.2011.07.012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lopez et al. - 2012 - The relationship between percentage of singletons and sampling effort A new approach to reduce the bias of richnes.pdf:pdf},
-journal = {Ecological Indicators},
-number = {1},
-pages = {164--169},
-title = {{The relationship between percentage of singletons and sampling effort: A new approach to reduce the bias of richness estimates}},
-volume = {14},
-year = {2012}
-}
-@article{Caswell1976,
-abstract = {The relation of community structure to community function is the subject of much ecological theorizing. Three approaches to the problem, based on cybernetics, control theory, and niche theory, can be identified. They concur in giving biological interactions a major role in the determination of community structure in general, and species diversity in particular. To examine this body of theory, I use a "neutral" model for community development, a model which eliminates completely the biological interactions in question. Comparison of the patterns of community structure resulting from this model with the structure of natural communities provides an estimate of the effect of the biotic interactions. This can then be compared to the theoretically predicted effects. The neutral model used was originally developed in population genetics. In the context in which it is used here, it describes the stochastic development of a set of noninteracting populations, which colonize a community, persist temporarily, and eventually become extinct. The model predicts the form of the distribution of relative abundances and of species area curves, and sample values of species diversity. Comparisons of the model's predictions with actual community structure are made across what are taken to be gradients in the importance of biological interaction (successional vs. climax communities, high variation vs. low variation environments, the temperate zone vs. the tropics), using data on birds, fish, trees and insects. The results clearly contradict some of the theories of community structure. In those situations where biological interactions are predicted to generate the greatest increase in species diversity, the neutral model analysis shows that diversity is in fact significantly lower than would be expected in the absence of such interactions. Some implications of these findings for community theory are discussed.},
-author = {Caswell, Hal},
-doi = {10.2307/1942257},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Caswell - 1976 - Community Structure A Neutral Model Analysis.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {327--354},
-title = {{Community Structure: A Neutral Model Analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1942257/abstract},
-volume = {46},
-year = {1976}
-}
-@article{Taylor1988,
-abstract = {Phenotypic plasticity and genotypic variation were studied in Agropyron repens L. (Beauv.) collected from populations in two grassland communities which differed in the length of time since the last major disturbance. Twenty genotypes were collected from each population. Each genotype was vegetatively propagated, and subjected to six different treatments in a greenhouse. Phenotypic plasticity and genotypic variability were measured as across- and within-treatment standardized variances respectively. Patterns of plasticity were measured by genotype correlations across treatments. The results were presented graphically by the regression method of Garbutt and Zangerl (1983). Analysis of variance revealed significant population, genotype and treatment effects. Significant positive correlations between magnitude and variability of performance were found for all characters. Phenotypic plasticity and magnitude of performance were generally greater in plants collected from the older established field. Evidence for greater specialization in the older population was suggested by negative correlations between performance in the most favorable and least favorable treatments and by greater dissimilarity of genotype response across treatments. A more variable phenotypic response across treatments (i.e., higher plasticity) for plants from the older population may therefore be a consequence of specialization and not an adaptive trait per se.},
-author = {Taylor, D. R. and Aarssen, Lonnie W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Taylor, Aarssen - 1988 - An interpretation of phenotypic plasticity in Agropyron repens.pdf:pdf},
-journal = {American Journal of Botany},
-pages = {401--413},
-title = {{An interpretation of phenotypic plasticity in Agropyron repens}},
-url = {https://www.jstor.org/stable/2443987},
-volume = {75},
-year = {1988}
-}
-@incollection{Pires1985,
-abstract = {Cited in OTS 01-25 report, Diego cites it as saying liana forests found on rim of Amazon basin},
-author = {Pires, J M and Prance, G T},
-booktitle = {Key environments: Amazonia},
-keywords = {liana forest},
-pages = {109--145},
-title = {{The vegetation types of the Brazilian Amazon}},
-year = {1985}
-}
-@article{Thioulouse1997,
-abstract = {We present ADE-4, a multivariate analysis and graphical display software. Multivariate analysis methods available in ADE-4 include usual one-table methods like principal component analysis and correspondence analysis, spatial data analysis methods (using a total variance decomposition into local and global components, analogous to Moran and Geary indices), discriminant analysis and within/between groups analyses, many linear regression methods including lowess and polynomial regression, multiple and PLS (partial least squares) regression and orthogonal regression (principal component regression), projection methods like principal component analysis on instrumental variables, canonical correspondence analysis and many other variants, coinertia analysis and the RLQ method, and several three-way table (k-table) analysis methods. Graphical display techniques include an automatic collection of elementary graphics corresponding to groups of rows or to columns in the data table, thus providing a very efficient way for automatic k-table graphics and geographical mapping options. A dynamic graphic module allows interactive operations like searching, zooming, selection of points, and display of data values on factor maps. The user interface is simple and homogeneous among all the programs; this contributes to make the use of ADE-4 very easy for non specialists in statistics, data analysis or computer science.},
-author = {Thioulouse, Jean and Chessel, Daniel and Dol{\'{e}}dec, Sylvain and Olivier, Jean-Michel},
-journal = {Statistics and Computing},
-number = {1},
-pages = {75--83},
-title = {{ADE-4: a multivariate analysis and graphical display software}},
-url = {http://pbil.univ-lyon1.fr/ADE-4/article{\_}statcomp1997.php},
-volume = {7},
-year = {1997}
-}
-@article{Stegen2011,
-abstract = {Understanding the influences of dispersal limitation and environmental filtering on the structure of ecological communities is a major challenge in ecology. Insight may be gained by combining phylogenetic, functional and taxonomic data to characterize spatial turnover in community structure ($\beta$-diversity). We develop a framework that allows rigorous inference of the strengths of dispersal limitation and environmental filtering by combining these three types of $\beta$-diversity. Our framework provides model-generated expectations for patterns of taxonomic, phylogenetic and functional $\beta$-diversity across biologically relevant combinations of dispersal limitation and environmental filtering. After developing the framework we compared the model-generated expectations to the commonly used "intuitive" expectation that the variance explained by the environment or by space will, respectively, increase monotonically with the strength of environmental filtering or dispersal limitation. The model-generated expectations strongly departed from these intuitive expectations: the variance explained by the environment or by space was often a unimodal function of the strength of environmental filtering or dispersal limitation, respectively. Therefore, although it is commonly done in the literature, one cannot assume that the strength of an underlying process is a monotonic function of explained variance. To infer the strength of underlying processes, one must instead compare explained variances to model-generated expectations. Our framework provides these expectations. We show that by combining the three types of $\beta$-diversity with model-generated expectations our framework is able to provide rigorous inferences of the relative and absolute strengths of dispersal limitation and environmental filtering. Phylogenetic, functional and taxonomic $\beta$-diversity can therefore be used simultaneously to infer processes by comparing their empirical patterns to the expectations generated by frameworks similar to the one developed here.},
-author = {Stegen, James C. and Hurlbert, Allen H.},
-doi = {10.1371/journal.pone.0020906},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stegen, Hurlbert - 2011 - Inferring ecological processes from taxonomic, phylogenetic and functional trait $\beta$-diversity.pdf:pdf},
-journal = {PloS one},
-number = {6},
-pages = {e20906},
-title = {{Inferring ecological processes from taxonomic, phylogenetic and functional trait $\beta$-diversity.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3117851{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {6},
-year = {2011}
-}
-@article{Liu2015,
-abstract = {Entropy theory has been increasingly applied in hydrology in both descriptive and inferential ways. However, little attention has been given to the small-sample condition widespread in hydrological practice, where either hydrological measurements are limited or are even nonexistent. Accordingly, entropy estimated under this condition may incur considerable bias. In this study, small-sample condition is considered and two innovative entropy estimators, the Chao–Shen (CS) estimator and the James–Stein-type shrinkage (JSS) estimator, are introduced. Simulation tests are conducted with common distributions in hydrology, that lead to the best-performing JSS estimator. Then, multi-scale moving entropy-based hydrological analyses (MM-EHA) are applied to indicate the changing patterns of uncertainty of streamflow data collected from the Yangtze River and the Yellow River, China. For further investigation into the intrinsic property of entropy applied in hydrological uncertainty analyses, correlations of entropy and other statistics at different time-scales are also calculated, which show connections between the concept of uncertainty and variability.},
-author = {Liu, Dengfeng and Wang, Dong and Wang, Yuankun and Wu, Jichun and Singh, Vijay P. and Zeng, Xiankui and Wang, Lachun and Chen, Yuanfang and Chen, Xi and Zhang, Liyuan and Gu, Shenghua},
-doi = {10.1016/j.jhydrol.2015.11.019},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liu et al. - 2016 - Entropy of hydrological systems under small samples Uncertainty and variability.pdf:pdf},
-journal = {Journal of Hydrology},
-pages = {163--176},
-title = {{Entropy of hydrological systems under small samples: Uncertainty and variability}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0022169415008951},
-volume = {532},
-year = {2016}
-}
-@article{Couteron2003,
-abstract = {Maps of plant individuals in (x, y) coordinates (i.e. point patterns) are currently analysed through statistical methods assuming a homogeneous distribution of points, and thus a constant density within the study area. Such an assumption is seldom met at the scale of a field plot whilst delineating less heterogeneous subplots is not always easy or pertinent. In this paper we advocate local tests carried out in quadrats partitioning the plot and having a size objectively determined via a trade-off between squared bias and variance. In each quadrat, the observed pattern of points is tested against complete spatial randomness (CSR) through a classical Monte-Carlo approach and one of the usual statistics. Local tests yield maps of p-values that are amenable to diversified subsequent analyses, such as computation of a variogram or comparison with covariates. Another possibility uses the frequency distribution of p-values to test the whole point pattern against the null hypothesis of an inhomogeneous Poisson process. The method was demonstrated by considering computer-generated inhomogeneous point patterns as well as maps of woody individuals in banded vegetation (tiger bush) in semi-arid West Africa. Local tests proved able to properly depict spatial relationships between neighbours in spite of heterogeneity/clustering at larger scales. The method is also relevant to investigate interaction between density and spatial pattern in the presence of resource gradients.},
-annote = {Article
-English
-J VEG SCI
-694ZA},
-author = {Couteron, Pierre and Seghieri, Josianne and Chadoeuf, Jo{\"{e}}l},
-doi = {10.1111/j.1654-1103.2003.tb02141.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Couteron, Seghieri, Chadoeuf - 2003 - A test for spatial relationships between neighbouring plants in plots of heterogeneous plant densi.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {163--172},
-title = {{A test for spatial relationships between neighbouring plants in plots of heterogeneous plant density}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2003.tb02141.x/abstract},
-volume = {14},
-year = {2003}
-}
-@article{Sohn2014,
-abstract = {This study examines the spatial distribution of manufacturing activities in Korea to introduce spatial distributional aspects to industry classifications. One hundred and sixty two administrative units in mainland Korea with 180 manufacturing sectors were analysed for this purpose. In the main analysis, the spatial distribution and association of individual sectors are examined using concentration and agglomeration measures, and 180 sectors are then classified along with the values of these measures. The classification is conducted using factor analysis for identifying groups of industries with a common spatial distribution pattern. The analysis identifies five major industry groups in terms of their spatial distribution patterns.},
-author = {Sohn, Jungyul},
-doi = {10.1111/area.12064},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sohn - 2014 - Industry classification considering spatial distribution of manufacturing activities.pdf:pdf},
-journal = {Area},
-number = {1},
-pages = {101--110},
-title = {{Industry classification considering spatial distribution of manufacturing activities}},
-url = {http://dx.doi.org/10.1111/area.12064},
-volume = {46},
-year = {2014}
-}
-@article{Gatti2017,
-abstract = {A central question about biodiversity is how so many species can coexist within the same ecosystem. The idea that ecological niches are critical for the maintenance of species diversity has received increasing support recently. However, a niche is often considered as something static, preconditioned, and unchanging. With the “Biodiversity-related Niches Differentiation Theory” (BNDT), we recently proposed that species themselves are the architects of biodiversity, by proportionally increasing the number of potentially available niches in a given ecosystem. Along similar lines, but independently, the idea of viewing an ecosystem of interdependent species as an emergent autocatalytic set (a self-sustaining network of mutually “catalytic” entities) was suggested, where one (group of) species enables the existence of (i.e., creates niches for) other species. Here, we show that biodiversity can indeed be considered a system of autocatalytic sets, and that this view offers a possible answer to the fundamental question of why so many species can coexist in the same ecosystem. In particular, we combine the two theories (BNDT and autocatalytic sets), and provide some simple but formal examples of how this would work.},
-author = {Gatti, Roberto Cazzolla and Hordijk, Wim and Kauffman, Stuart},
-doi = {10.1016/j.ecolmodel.2016.12.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gatti, Hordijk, Kauffman - 2017 - Biodiversity is autocatalytic.pdf:pdf},
-journal = {Ecological Modelling},
-pages = {70--76},
-title = {{Biodiversity is autocatalytic}},
-url = {http://dx.doi.org/10.1016/j.ecolmodel.2016.12.003},
-volume = {346},
-year = {2017}
-}
-@article{Norden2017,
-abstract = {Whether successional forests converge towards an equilibrium in species composition remains an elusive question, hampered by high idiosyncrasy in successional dynamics. Based on long-term tree monitoring in second-growth (SG) and old-growth (OG) forests in Costa Rica, we show that patterns of convergence between pairs of forest stands depend upon the relative abundance of species exhibiting distinct responses to the successional gradient. For instance, forest generalists contributed to convergence between SG and OG forests, whereas rare species and old-growth specialists were a source of divergence. Overall, opposing trends in taxonomic similarity among different subsets of species nullified each other, producing a net outcome of stasis over time. Our results offer an explanation for the limited convergence observed between pairwise communities and suggest that rare species and old-growth specialists may be prone to dispersal limitation, while the dynamics of generalists and second-growth specialists are more predictable, enhancing resilience in tropical secondary forests.},
-author = {Norden, Natalia and Boukili, Vanessa and Chao, Anne and Ma, K. H. and Letcher, Susan G. and Chazdon, Robin L.},
-doi = {10.1111/ele.12852},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Norden et al. - 2017 - Opposing mechanisms affect taxonomic convergence between tree assemblages during tropical forest succession.pdf:pdf},
-journal = {Ecology Letters},
-number = {11},
-pages = {1448--1458},
-title = {{Opposing mechanisms affect taxonomic convergence between tree assemblages during tropical forest succession}},
-volume = {20},
-year = {2017}
-}
-@article{Violle2014,
-abstract = {Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.},
-author = {Violle, Cyrille and Reich, Peter B. and Pacala, Stephen W. and Enquist, Brian J. and Kattge, Jens},
-doi = {10.1073/pnas.1415442111},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Violle et al. - 2014 - The emergence and promise of functional biogeography.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences},
-number = {38},
-pages = {13690--13696},
-title = {{The emergence and promise of functional biogeography}},
-volume = {111},
-year = {2014}
-}
-@article{Callejon1997,
-abstract = {Con las medidas tradicionales de concentraci{\'{o}}n geogr{\'{a}}fica de la industria no es posible discriminar en qu{\'{e}} grado influyen las econom{\'{i}}as externas de aglomeraci{\'{o}}n en las pautas de concentraci{\'{o}}n. Ellison y Glaeser han propuesto un {\'{i}} ndice que mide el grado de “localizaci{\'{o}}n” de las industrias, es decir, en qu{\'{e}} grado influyen las econom{\'{i}}as de aglomeraci{\'{o}}n en las decisiones de localizaci{\'{o}}n de las empresas. En este trabajo se hace una aplicaci{\'{o}}n a Espa{\~{n}}a del mencionado {\'{i}}ndice. Se comprueba que, efectivamente, los sectores industriales difieren ampliamente en su grado de localizaci{\'{o}}n; y que entre 1981 y 1992 no se produjo en Espa{\~{n}}a una tendencia significativa hacia una mayor concentraci{\'{o}}n geogr{\'{a}}fica de la industria.},
-author = {Callej{\'{o}}n, M},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Callej{\'{o}}n - 1997 - Concentraci{\'{o}}n Geogr{\'{a}}Fica de la Industria y Econom{\'{i}}as de Aglomeraci{\'{o}}n.pdf:pdf},
-journal = {Economia Industrial},
-number = {5},
-pages = {61--68},
-title = {{Concentraci{\'{o}}n Geogr{\'{a}}fica de la Industria y Econom{\'{i}}as de Aglomeraci{\'{o}}n}},
-volume = {317},
-year = {1997}
-}
-@article{Bellet1999,
-author = {Bellet, Michel and Lallich, St{\'{e}}phane},
-journal = {Economie Appliqu{\'{e}}e},
-number = {4},
-pages = {7--33},
-title = {{Externalit{\'{e}}s, mod{\`{e}}le input-output et {\'{e}}conomie de l'innovation: quelques enseignements}},
-volume = {LII},
-year = {1999}
-}
-@book{Henderson2004,
-address = {Amsterdam},
-author = {Henderson, J. Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-publisher = {Elsevier. North Holland},
-title = {{Handbook of Urban and Regional Economics}},
-year = {2004}
-}
-@book{Florence1972,
-address = {London},
-author = {Florence, Philip Sargant},
-edition = {3rd ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Florence - 1972 - The Logic of British and American Industry A Realistic Analysis of Economic Structure and Government.pdf:pdf},
-publisher = {Routledge {\&} Kegan Paul},
-title = {{The Logic of British and American Industry: A Realistic Analysis of Economic Structure and Government}},
-year = {1972}
-}
-@article{Chao2008,
-abstract = {A traditional approach for assessing similarity among N (N {\textgreater} 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N - 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.},
-annote = {Times Cited: 10},
-author = {Chao, Anne and Jost, Lou and Chiang, S. C. and Jiang, Y. H. and Chazdon, Robin L.},
-doi = {10.1111/j.1541-0420.2008.01010.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2008 - A Two-Stage Probabilistic Approach to Multiple-Community Similarity Indices.pdf:pdf},
-journal = {Biometrics},
-number = {4},
-pages = {1178--1186},
-title = {{A Two-Stage Probabilistic Approach to Multiple-Community Similarity Indices}},
-volume = {64},
-year = {2008}
-}
-@article{Pelissier2001,
-abstract = {Spatial heterogeneity is a characteristic of most natural ecosystems which is difficult to handle analytically, particularly in the absence of knowledge about the exogenous factors responsible for this heterogeneity. While classical methods for analysis of spatial point patterns usually require the hypothesis of homogeneity, we present a practical ap- proach for partitioning heterogeneous vegetation plots into homogeneous subplots in simple cases of heterogeneity with- out drastically reducing the data. It is based on the detection of endogenous variations of the pattern using local density and second-order local neighbour density functions that allow delineation of irregularly shaped subplots that could be con- sidered as internally homogeneous. Spatial statistics, such as Ripley's K-function adapted to analyse plots of irregular shape, can then be computed for each of the homogeneous subplots. Two applications to forest ecological field data demonstrate that the method, addressed to ecologists, can avoid misinter- pretations of the spatial structure of heterogeneous vegetation stands},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l and Goreaud, Fran{\c{c}}ois},
-doi = {10.1023/A:1011122218548},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/P{\'{e}}lissier, Goreaud - 2001 - A practical approach to the study of spatial structure in simple cases of heterogeneous vegetation.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {1},
-pages = {99--108},
-title = {{A practical approach to the study of spatial structure in simple cases of heterogeneous vegetation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2001.tb02621.x/abstract},
-volume = {12},
-year = {2001}
-}
-@article{Acs1994,
-abstract = {The findings in this paper provide some insight into how small firms are able to innovate. Using a production function approach to relate knowledge generating inputs to innovative output, the empirical results suggest that small firms are the recipients of R{\&}D spillovers from knowledge generated in the R{\&}D centers of their larger counterparts and in universities. Such R{\&}D spillovers are apparently more decisive in promoting the innovative activity of small firms than of large corporations.},
-author = {Acs, Zoltan J. and Audretsch, David B. and Feldman, Maryann P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Acs, Audretsch, Feldman - 1994 - R{\&}D Spillovers and Recipient Firm Size.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {2},
-pages = {336--340},
-title = {{R{\&}D Spillovers and Recipient Firm Size}},
-url = {http://www.jstor.org/stable/2109888},
-volume = {76},
-year = {1994}
-}
-@article{Carmona2014,
-abstract = {Ecologists use approaches based on plant functional traits to tackle several fundamental and applied questions. Although a perfect characterization of functional trait structure requires the measurement of all the individuals in communities, this is prohibitively resource-consuming. Consequently, the general practice is to average the trait values of a reduced number of individuals per species. However, there are different alternatives regarding the number, identity and spatial location of the individuals chosen to calculate species-averaged trait values. In this study, we compared different strategies for sampling functional traits, using community-weighted mean trait values (CWM) and the Rao index of functional diversity (FD). We intensively sampled the functional trait structure along a topographical gradient in a Mediterranean grassland, obtaining accurate estimations of the ‘real' values of these indices (CWMI and FDI) for three traits (height, leaf area and specific leaf area). We simulated three different sampling strategies differing in the spatial location of the individuals used to estimate species-mean trait: (i) average of the whole gradient (GLO), (ii) average of the sampling unit in which the abundances of species maximize (MAX) and (iii) average of a reduced number of individuals per species and sampling unit (LOC). For each strategy, we simulated different sampling intensities (number of individuals sampled). For each trait, we examined the ability of each strategy and sampling intensity to accurately estimate CWMI and FDI, as well as their ability to detect changes in functional trait structure along the topographical gradient. LOC outperformed the other strategies in terms of accuracy and bias, and was much more efficient to describe changes along the gradient, regardless of the traits and indicators considered. Furthermore, LOC was the only strategy that improved consistently as sampling intensity increased, especially at low levels of intensity. Our results indicate that the impact of considering intraspecific variability in trait values can be greater than commonly assumed. Strategies that neglect this source of variability can result in inaccurate or biased estimations of the functional trait structure of plant communities. Most importantly, we show that intraspecific variability can be taken into consideration without any increases in the total number of individuals measured.},
-author = {Carmona, Carlos P. and Rota, Cristina and Azc{\'{a}}rate, Francisco M. and Peco, Bego{\~{n}}a},
-doi = {10.1111/1365-2435.12366},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carmona et al. - 2014 - More for less sampling strategies of plant functional traits across local environmental gradients.pdf:pdf},
-journal = {Functional Ecology},
-number = {4},
-pages = {579--588},
-title = {{More for less : sampling strategies of plant functional traits across local environmental gradients}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12366/abstract},
-volume = {29},
-year = {2015}
-}
-@article{Cromley2012,
-abstract = {Location quotients (LQs) are commonly used descriptive statistics in spatial analysis. They are not directly affected by neighbor relationships, and their calculation ignores spatial information. This article computes LQs as focal, rather than strictly local, functions by incorporating the spatial structure of the observations in the reference group in their computation. Focal LQs, tested for significance by event-based Monte Carlo simulations, are applied both to North Carolina sudden infant death syndrome data for comparison with the G(i)* spatial statistic and to sectoral employment data in that state in a more typical context for LQ analysis. The significance tests show that the focal LQ is far more sensitive to the size of the denominator for spatially intensive data than is the G(i)* statistic.},
-annote = {ISI Document Delivery No.: 015MH
-Times Cited: 0
-Cited Reference Count: 25
-Cromley, Robert G. Hanink, Dean M.
-Wiley-blackwell
-Hoboken},
-author = {Cromley, Robert G. and Hanink, Dean M.},
-doi = {10.1111/j.1538-4632.2012.00852.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cromley, Hanink - 2012 - Focal Location Quotients Specification and Applications.pdf:pdf},
-journal = {Geographical Analysis},
-number = {4},
-pages = {398--410},
-title = {{Focal Location Quotients: Specification and Applications}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.2012.00852.x/abstract},
-volume = {44},
-year = {2012}
-}
-@article{Louvet2015,
-abstract = {Using the R language as a GIS applied on forest fire data in South of France, the goal of the research is to emphasize how spatial statistics may depend on the areal units chosen. First, we propose to map the forest fire data at different scale levels based on administrative boundaries. Second, we measure the MAUP by showing scale sensitivity in descriptive statistics and in regression analyses. Finally, although many tools can be used for vector or raster data aggregation and mapping, we discuss why we choose R as a primary analysis tool and R added-value.},
-author = {Louvet, Romain and Aryal, Jagannath and Josselin, Didier and Genre-Grandpierre, Cyrille},
-doi = {10.1016/j.proenv.2015.07.118},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Louvet et al. - 2015 - R as a GIS Illustrating Scale and Aggregation Problems with Forest Fire Data.pdf:pdf},
-journal = {Procedia Environmental Sciences},
-pages = {66--69},
-title = {{R as a GIS: Illustrating Scale and Aggregation Problems with Forest Fire Data}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1878029615003308},
-volume = {27},
-year = {2015}
-}
-@article{May2000,
-author = {May, Robert M. and Stumpf, Michael P. H.},
-doi = {10.1126/science.290.5499.2084},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May, Stumpf - 2000 - Species-Area Relations in Tropical Forests.pdf:pdf},
-journal = {Science},
-number = {5499},
-pages = {2084--2086},
-title = {{Species-Area Relations in Tropical Forests}},
-url = {http://www.sciencemag.org/content/290/5499/2084.short},
-volume = {290},
-year = {2000}
-}
-@article{Gregorius2014,
-abstract = {It is routinely understood that the total diversity within a metacommunity (? -diversity) can be partitioned into one component summarizing the diversity within communities (a-diversity) and a second component representing the contribution of diversity (or differences) between communities ({\ss}-diversity). The underlying thought is that merging differentiated communities should raise the total diversity above the average level of diversity within the communities. The crucial point in this partitioning criterion is set by the notion of “diversity within communities” (DWC) and its relation to the total diversity. The common approach to summarizing DWC is in terms of averages. Yet there are many different ways to average diversity, and not all of these averages stay below the total diversity for every measure of diversity, corrupting the partitioning criterion. This raises the question of whether conceptual properties of diversity measures exist, the fulfillment of which implies that all measures of DWC obey the partitioning criterion. It is shown that the straightforward generalization of the plain counting of types (richness) leads to a generic diversity measure that has the desired properties and, together with its effective numbers, fulfills the partitioning criterion for virtually all of the relevant diversity measures in use. It turns out that the classical focus on DWC (a) and its complement ({\ss} as derived from a and ? ) in the partitioning of total diversity captures only the apportionment perspective of the distribution of trait diversity over communities (which implies monomorphism within communities at the extreme). The other perspective, differentiation, cannot be assessed appropriately unless an additional level of diversity is introduced that accounts for differences between communities (such as the joint “type-community diversity”). Indices of apportionment IA (among which is GST and specially normalized versions of {\ss}) and differentiation ID are inferred, and it is demonstrated that conclusions derived from IA depend considerably on the measure of diversity to which it is applied, and that in most cases an assessment of the distribution of diversity over communities requires additional computation of ID.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.5194/we-14-51-2014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 2014 - Partitioning of diversity the within communities component.pdf:pdf},
-journal = {Web Ecology},
-pages = {51--60},
-title = {{Partitioning of diversity : the "within communities" component}},
-volume = {14},
-year = {2014}
-}
-@misc{Rysman2003,
-author = {Rysman, Marc and Greenstein, Shane},
-booktitle = {mimeo},
-keywords = {Rysman (2003).pdf},
-mendeley-tags = {Rysman (2003).pdf},
-title = {{A Note on Testing for Agglomeration and Dispersion}},
-url = {http://econ.bu.edu/rysman/research/aggdis2.pdf},
-year = {2003}
-}
-@article{Chisholm2013,
-abstract = {1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which repre- sent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8–50 ha from across the world. The data were collected using standardized protocols, obvi- ating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04 ha) species richness was generally positively related to pro- ductivity and biomass within plots, with a doubling of species richness corresponding to an average 48{\%} increase in productivity and 53{\%} increase in biomass. At larger spatial grains (0.25 ha, 1 ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04 ha spatial grain, a doubling of species richness corre- sponded to a 5{\%} increase in productivity and 7{\%} increase in biomass. Productivity and biomass were them- selves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productiv- ity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consis- tent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04 ha) to slightly larger scales (0.25 and 1 ha). This needs to be recognized in forest conservation policy and management.},
-author = {Chisholm, Ryan A. and Muller-Landau, Helene C. and {Abdul Rahman}, Kassim and Bebber, Daniel P. and Bin, Yue and Bohlman, Stephanie A. and Bourg, Norman A. and Brinks, Joshua and Bunyavejchewin, Sarayudh and Butt, Nathalie and Cao, Honglin and Cao, Min and C{\'{a}}rdenas, Dairon and Chang, Li-Wan and Chiang, Jyh-Min and Chuyong, George B. and Condit, Richard and Dattaraja, Handanakere S. and Davies, Stuart and Duque, Alvaro and Fletcher, Christine and Gunatilleke, Nimal and Gunatilleke, Savitri and Hao, Zhanqing and Harrison, Rhett D. and Howe, Robert and Hsieh, Chang-Fu and Hubbell, Stephen P. and Itoh, Akira and Kenfack, David and Kiratiprayoon, Somboon and Larson, Andrew J. and Lian, Juyu and Lin, Dunmei and Liu, Haifeng and Lutz, James A. and Ma, Keping and Malhi, Yadvinder and McMahon, Sean and McShea, William and Meegaskumbura, Madhava and {Mohd. Razman}, Salim and Morecroft, Michael D. and Nytch, Christopher J. and Oliveira, Alexandre and Parker, Geoffrey G. and Pulla, Sandeep and Punchi-Manage, Ruwan and Romero-Saltos, Hugo and Sang, Weiguo and Schurman, Jon and Su, Sheng-Hsin and Sukumar, Raman and Sun, I-Fang and Suresh, Hebbalalu S. and Tan, Sylvester and Thomas, Duncan and Thomas, Sean and Thompson, Jill and Valencia, Renato and Wolf, Amy and Yap, Sandra and Ye, Wanhui and Yuan, Zuoqiang and Zimmerman, Jess K.},
-doi = {10.1111/1365-2745.12132},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chisholm et al. - 2013 - Scale-dependent relationships between tree species richness and ecosystem function in forests.pdf:pdf},
-journal = {Journal of Ecology},
-number = {5},
-pages = {1214--1224},
-title = {{Scale-dependent relationships between tree species richness and ecosystem function in forests}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12132},
-volume = {101},
-year = {2013}
-}
-@article{Mack2013,
-abstract = {The industrial composition of places has received considerable attention because of the widespread belief that industrial diversity buffers regional economies from economic shocks. Subsequently, a variety of toolkits and indices have been developed with the goal of better capturing the compositional dynamics of regions. Although useful, a key drawback of these indices is their static nature, which limits the utility of these indices in a space–time context. This paper provides an overview of and applications of an interface called interactive visualization tool for indices of industrial diversity, which is a visual analytics tool developed specifically for the analysis and visualization of local measures of industrial composition for areal data. This overview will include a discussion of its key features, as well as a demonstration of the utility of the interface in exploring questions surrounding diversity and the dynamic nature of composition through space and time. A focus of this demonstration is to highlight how the interactivity and query functionality of this interface overcome several of the obstacles to understanding composition through space and time that prior toolkits and comparative static approaches have been unable to address.},
-author = {Mack, Elizabeth A. and Zhang, Yifan and Rey, Sergio and Maciejewski, Ross},
-doi = {10.1007/s10109-013-0193-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mack et al. - 2013 - Spatio-temporal analysis of industrial composition with IVIID an interactive visual analytics interface for industr.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {2},
-pages = {183--209},
-title = {{Spatio-temporal analysis of industrial composition with IVIID: an interactive visual analytics interface for industrial diversity}},
-url = {http://link.springer.com/10.1007/s10109-013-0193-4},
-volume = {16},
-year = {2013}
-}
-@article{Pelissier1998,
-abstract = {In a primary dense moist evergreen forest of southern India, spatial patterns of trees ≥30 cm gbh were investigated from three contrasting 0.4-ha plots that differed in topography and amount of disturbance due to treefall. Exploratory data analysis is based on second-order neighbourhood and pair-correlation statistics used to describe the degree of clustering/regularity in patterns of all trees, and the degree of attraction/repulsion between young trees and adults. Stochastic simulations from the Markov point process models are then used to fit spatial interaction models. The results show that spatial patterns can be related to particular dynamic processes which depend on both exogenous and endogenous factors: on steep slopes disturbed by many treefalls, spatial pattern displays large clusters which can be interpreted as within-gap regeneration stages of various ages, while in areas undisturbed over a long period, interactions between young trees and adults give rise to spatial patterns consistent with substitution dynamic processes implying standing mortality rather than treefalls. Characterizing forest dynamics through spatial patterns of trees opens up the possibility of mapping structural units that might be considered as elementary functional patches of the forest mosaic.},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/P{\'{e}}lissier - 1998 - Tree spatial patterns in three contrasting plots of a southern Indian tropical moist evergreen forest.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {1},
-pages = {1--16},
-title = {{Tree spatial patterns in three contrasting plots of a southern Indian tropical moist evergreen forest}},
-url = {https://www.jstor.org/stable/2559862},
-volume = {14},
-year = {1998}
-}
-@book{Aczel1975,
-address = {New York},
-author = {Acz{\'{e}}l, J. and Dar{\'{o}}czy, Zolt{\'{a}}n},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Acz{\'{e}}l, Dar{\'{o}}czy - 1975 - On measures of information and their characterizations.pdf:pdf},
-pages = {234},
-publisher = {Academic Press},
-title = {{On measures of information and their characterizations}},
-year = {1975}
-}
-@article{Vane-Wright1991,
-abstract = {Politicians and scientists alike now agree that a priority list of global centres for preservationof biological diversity is required. Diversity has generally been measured only in terms of species richness, or in the form of indices combining richness with abundance. Such measures are considered inadequate for the task in hand. A novel index, based on the information content of cladistic classifications and giving a measure of taxonomic distinctness, is introduced. This taxic diversity measure, when coupled with detailed knowledge of distribution, can be used in modified analyses of the type previously developed as ‘critical faunas analysis' or ‘network analysis'. Central to all such analyses is the concept of complementarity of floras or faunas. By employing complementariry, step-wise procedures can identify optimally efficient, single-site sequences of priority areas for a group, taking existing reserves into account or not, as required. For practical planning it is concluded that two basic rounds of analysis are required: first, recognition of global priority areas by taxic diversity techniques; secondly, within any such area, analysis without taxic weighting (as being developed by Margules and his co-workers) to identify a network of reserves to contain all local taxa and ecosystems. The paper concludes with a brief discussion of some immediate prospects for development of a systematic approach to global conservation evaluation.},
-author = {Vane-Wright, R. I. and Humphries, C. J. and Williams, P. H.},
-doi = {10.1016/0006-3207(91)90030-D},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vane-Wright, Humphries, Williams - 1991 - What to protect—Systematics and the agony of choice.pdf:pdf},
-journal = {Biological Conservation},
-number = {3},
-pages = {235--254},
-title = {{What to protect?—Systematics and the agony of choice}},
-url = {http://www.sciencedirect.com/science/article/pii/000632079190030D},
-volume = {55},
-year = {1991}
-}
-@article{Velazquez2016,
-abstract = {Over the last two decades spatial point pattern analysis (SPPA) has become increasingly popular in ecological research. To direct future work in this area we review studies using SPPA techniques in ecology and related disciplines. We first summarize the key elements of SPPA in ecology (i.e., data types, summary statistics and their estimation, null models, comparison of data and models, and consideration of heterogeneity); second, we review how ecologists have used these key elements; and finally, we identify practical difficulties that are still commonly encountered and point to new methods that allow current key questions in ecology to be effectively addressed. Our review of 308 articles published over the period 1992-2012 reveals that a standard canon of SPPA techniques in ecology has been largely identified and that most of the earlier technical issues that occupied ecologists, such as edge correction, have been solved. However, the majority of studies underused the methodological potential offered by modern SPPA. More advanced techniques of SPPA offer the potential to address a variety of highly relevant ecological questions. For example, inhomogeneous summary statistics can quantify the impact of heterogeneous environments, mark correlation function can include trait and phylogenetic information in the analysis of multivariate spatial patterns, and more refined point process models can be used to realistically characterize the structure of a wide range of patterns. Additionally, recent advances in fitting spatially-explicit simulation models of community dynamics to point pattern summary statistics hold the promise for solving the longstanding problem of linking pattern to process. All these newer developments allow ecologists to keep up with the increasing availability of spatial data sets provided by newer technologies, which allow point patterns and environmental variables to be mapped over large spatial extents at increasingly higher image resolutions.},
-author = {Vel{\'{a}}zquez, Eduardo and Mart{\'{i}}nez, Isabel and Getzin, Stephan and Moloney, Kirk A. and Wiegand, Thorsten},
-doi = {10.1111/ecog.01579},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vel{\'{a}}zquez et al. - 2016 - An evaluation of the state of spatial point pattern analysis in ecology(2).pdf:pdf},
-journal = {Ecography},
-number = {11},
-pages = {1042--1055},
-title = {{An evaluation of the state of spatial point pattern analysis in ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.01579/abstract},
-volume = {39},
-year = {2016}
-}
-@article{Legendre2014a,
-abstract = {This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.},
-author = {Legendre, Pierre and Gauthier, Olivier},
-doi = {10.1098/rspb.2013.2728},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Gauthier - 2014 - Statistical methods for temporal and space − time analysis of community composition data Statistical methods.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-pages = {20132728},
-title = {{Statistical methods for temporal and space − time analysis of community composition data Statistical methods for temporal and space – time analysis of community composition data †}},
-volume = {281},
-year = {2014}
-}
-@article{Allan1975,
-abstract = {The information theory measure H is partitioned into components to allow evaluation of various contributions to total diversity. If a species collection is sampled at several microhabitats within each of several sites, we may ask whether the niche breadth of a particular species, and the diversity of the entire collection, are greater with respect to microhabitats or sites. The usefulness of these measures is discussed in the context of within-habitat and between-habitat contributions to diversity.},
-author = {Allan, J. D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Allan - 1975 - Components of Diversity.pdf:pdf},
-journal = {Oecologia},
-number = {4},
-pages = {359--367},
-title = {{Components of Diversity}},
-url = {https://www.jstor.org/stable/4215087},
-volume = {18},
-year = {1975}
-}
-@article{Preston1948,
-annote = {ArticleType: research-article / Full publication date: Jul., 1948 / Copyright {\^{A}}{\textcopyright} 1948 Ecological Society of America},
-author = {Preston, F. W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Preston - 1948 - The Commonness, And Rarity, of Species.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {254--283},
-title = {{The Commonness, And Rarity, of Species}},
-url = {http://www.jstor.org/stable/1930989},
-volume = {29},
-year = {1948}
-}
-@article{Reich2014,
-abstract = {*$\backslash$nThe leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade-off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources.$\backslash$n$\backslash$n$\backslash$n$\backslash$n*$\backslash$nEvidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages).$\backslash$n$\backslash$n$\backslash$n$\backslash$n*$\backslash$nThere are linkages across organs and coupling among resources, resulting in an integrated whole-plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species.$\backslash$n$\backslash$n$\backslash$n$\backslash$n*$\backslash$nEconomic traits influence performance and fitness consistent with trait-based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates.$\backslash$n$\backslash$n$\backslash$n$\backslash$n*$\backslash$nSynthesis. Traits matter. A single ‘fast–slow' plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.},
-author = {Reich, Peter B.},
-doi = {10.1111/1365-2745.12211},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {275--301},
-title = {{The world-wide 'fast-slow' plant economics spectrum: A traits manifesto}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12211/abstract},
-volume = {102},
-year = {2014}
-}
-@article{Clapham1936,
-author = {Clapham, A. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clapham - 1936 - Over-dispersion in grassland communities and the use of statistical methods in plant ecology.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {232--251},
-title = {{Over-dispersion in grassland communities and the use of statistical methods in plant ecology}},
-volume = {24},
-year = {1936}
-}
-@article{Pakeman2014,
-abstract = {1. Functional diversity (FD) is an important concept for studies of both ecosystem processes and community assembly, so it is important to understand the behaviour of common metrics used to express it. 2. Data from an existing study of the relationship between FD and environmental drivers were used to simulate the impact of a progressive failure to measure the traits of all the species present under three scenarios: intraspecific variation between sites ignored (i), assessed (ii) or (iii) ignored but with metrics calculated at the sampling unit rather than the site level. 3. All the FD metrics were highly sensitive to failing to measure the traits of all the species present. Functional dispersion, functional richness and Rao's entropy all generally declined with a reduced proportion of species or cover assessed for traits, whilst functional divergence and evenness increased for some sites and decreased for others. Functional richness was the most sensitive (mean absolute deviation at 70{\%} of species assessed had a range of 11.2–28.2{\%} across scenarios), followed by functional evenness (range 6.4–38.5{\%}), functional divergence (5.2–8.3{\%}), Rao's entropy (1.4–7.0{\%}) and functional dispersion (0.7–3.5{\%}). 4. It is clear that failing to measure the traits of all species at a site can have a serious impact on the value of any functional trait metric computed and on any conclusions drawn from such data. Future studies of FD need to concentrate on the potential impact of the sampling regime of both traits and species and the scale at which the computations are made on the behaviour of metrics and subsequent robustness of the results.},
-author = {Pakeman, Robin J.},
-doi = {10.1111/2041-210X.12136},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {1},
-title = {{Functional trait metrics are sensitive to the completeness of the species' trait data?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12136/abstract},
-volume = {5},
-year = {2014}
-}
-@article{Ricotta2005d,
-abstract = {Functional diversity (FD) has been seen as the key to understanding ecosystem processes, such as productivity, nutrient cycling and storage, carbon sequestration, and stability to perturbations. Yet it is still unclear how FD should be measured. In this paper, I propose a set of fundamental criteria that a meaningful index of FD should satisfy to reasonably behave in ecological research. If FD is computed from the pairwise functional distances among the species of a given assemblage, the candidate measures should be set monotone, monotone in distance, and should conform to the twinning property. On the other hand, if FD is computed taking into account both the pairwise functional distances among species and their relative abundances, the candidate measure should be concave, thus allowing additive diversity decomposition into $\alpha$- $\beta$- and $\gamma$-terms. Conformity to the above requirements may be beneficial for selecting a family of measures that are most appropriate for a correct evaluation of the relations between biological diversity and ecosystem functioning. {\textcopyright} 2005 Gesellschaft f{\"{u}}r {\"{O}}kologie. Published by Elsevier GmbH. All rights reserved.},
-annote = {Cited By (since 1996):75
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: BAEAC
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1016/j.baae.2005.02.008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2005 - A note on functional diversity measures.pdf:pdf},
-journal = {Basic and Applied Ecology},
-number = {5},
-pages = {479--486},
-title = {{A note on functional diversity measures}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-25144468858{\&}partnerID=40{\&}md5=679d86e2df8d33eaeae0f57377ad1aac},
-volume = {6},
-year = {2005}
-}
-@article{Baselga2010,
-abstract = {Aim Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns. Innovation I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns. Main conclusion Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.},
-annote = {ISI Document Delivery No.: 530FA
-Baselga, Andres
-WILEY-BLACKWELL PUBLISHING, INC},
-author = {Baselga, Andr{\'{e}}s},
-doi = {10.1111/j.1466-8238.2009.00490.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baselga - 2010 - Partitioning the turnover and nestedness components of beta diversity.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {1},
-pages = {134--143},
-title = {{Partitioning the turnover and nestedness components of beta diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2009.00490.x/abstract},
-volume = {19},
-year = {2010}
-}
-@article{ChanderbaliA.S.vanderWerffH.Renner2001,
-author = {{Chanderbali, A. S., van der Werff, H., Renner}, S. S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chanderbali, A. S., van der Werff, H., Renner - 2001 - Phylogeny and historical biogeography of Lauraceae evidence from the chloroplast.pdf:pdf},
-journal = {Ann. Missouri Bot. Gard.},
-number = {1},
-pages = {104--134},
-title = {{Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes}},
-volume = {88},
-year = {2001}
-}
-@book{Hubbell2001b,
-abstract = {unified-neutral-theory-biodiversity.pdf; The unified neutral theory of biodiversity and biogeography (here "Unified Theory" or "UNTB") is a hypothesis and the title of a monograph [1] by ecologist Stephen Hubbell. The hypothesis aims to explain the diversity and relative abundance of species in ecological communities, although like other neutral theories of ecology, Hubbell's hypothesis assumes that the differences between members of an ecological community of trophically similar species are "neutral," or irrelevant to their success.},
-author = {Hubbell, S P},
-booktitle = {Monographs in Population Biology},
-doi = {10.1016/j.tree.2011.03.024},
-isbn = {0691021295},
-issn = {0169-5347},
-pages = {375},
-pmid = {21561679},
-title = {{The Unified Neutral Theory of Biodiversity and Biography}},
-volume = {32},
-year = {2001}
-}
-@article{Fortunel2014,
-abstract = {The consequences of biodiversity loss for ecosystem services largely depend on the functional identities of extirpated species. However, poor descriptions of spatial patterns of community functional composition across landscapes hamper accurate predictions, particularly in highly diverse tropical regions. Therefore, understanding how community functional composition varies across environmental gradients remains an important challenge. We sampled 15 functional traits in 800 Neotropical tree species across 13 forest plots representative of the broad climatic and soil gradients encompassed by three widespread lowland forest habitats (terra firme forests on clay-rich soils, seasonally flooded forests and white-sand forests) at opposite ends of Amazonia (Peru and French Guiana). We combined univariate and multivariate approaches to test the magnitude and predictability of environmental filtering on community leaf and wood functional composition. Directional shifts in community functional composition correlated with environmental changes across the 13 plots, with denser leaves, stems and roots in forests occurring in environments with limited water and soil-nutrient availability. Critically, these relationships allowed us to accurately predict the functional composition of 61 additional forest plots from environmental data alone. Synthesis. Environmental filtering consistently shapes the functional composition of highly diverse tropical forests at large scales across the terra firme, seasonally flooded and white-sand forests of lowland Amazonia. Environmental factors drive and allow the prediction of variation in community functional composition among habitat types in Amazonian forests. {\textcopyright} 2013 British Ecological Society.},
-author = {Fortunel, Claire and Paine, C. E. Timothy and Fine, Paul V. A. and Kraft, Nathan J. B. and Baraloto, Christopher},
-doi = {10.1111/1365-2745.12160},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fortunel et al. - 2014 - Environmental factors predict community functional composition in Amazonian forests.pdf:pdf},
-journal = {Journal of Ecology},
-pages = {145--155},
-title = {{Environmental factors predict community functional composition in Amazonian forests}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12160/abstract},
-volume = {102},
-year = {2014}
-}
-@article{Lande1996,
-abstract = {pecies richness, Shannon information, and Simpson diversity are the three most commonly used nonparametric measures of species diversity. The sampling bias and variance of these measures differ greatly. Species richness may be seriously underestimated for even very large samples from a speciose community. The bias in species richness and Shannon information depend on unknown parameters of the species abundance distribution. An unbiased estimator exists only for Simpson diversity. Each of these measures is concave, so that the total diversity in a pooled set of communities exceeds (or equals) the average diversity within communities. The total diversity in a set of communities can therefore be partitioned into positive, additive components within and among communities, corresponding to $\alpha$- and $\beta$-diversity. Partitioning Simpson diversity corresponds to an analysis of variance. The proportion of the total diversity found within communities provides a natural measure of similarity among multiple communities. The expected similarity among multiple random samples from the same community depends on the number of samples and on the underlying measure of diversity.},
-author = {Lande, Russell},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lande - 1996 - Statistics and partitioning of species diversity, and similarity among multiple communities.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {5--13},
-title = {{Statistics and partitioning of species diversity, and similarity among multiple communities}},
-volume = {76},
-year = {1996}
-}
-@article{Guan2009a,
-abstract = {We introduce new variance estimation procedures for second-order statistics that are computed from a single realization of intensity reweighted stationary spatial point processes. The statistics are defined either on a subset B of the observation window or on the whole window. For the former, we use subblocks that have the same size and shape as B as "replicates" of B in order to estimate the target variance. For the latter, we develop a subsampling estimator for a key component in the target variance and estimate its other components by method-of-moment methods. Under some suitable conditions, we prove that the proposed variance estimators are consistent for the target variances in both cases. Simulations and an application to a real data example are used to demonstrate the usefulness of the proposed methods. This article has supplementary material online. {\textcopyright} 2009 American Statistical Association.},
-annote = {cited By (since 1996) 2},
-author = {Guan, Yontao},
-doi = {10.1198/jasa.2009.tm08541},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2009 - On nonparametric variance estimation for second-order statistics of inhomogeneous spatial point processes with a known par.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {488},
-pages = {1482--1491},
-title = {{On nonparametric variance estimation for second-order statistics of inhomogeneous spatial point processes with a known parametric intensity form}},
-volume = {104},
-year = {2009}
-}
-@article{Marcon2015a,
-author = {Marcon, Eric},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon - 2015 - Practical Estimation of Diversity from Abundance Data.pdf:pdf},
-journal = {HAL},
-number = {version 2},
-title = {{Practical Estimation of Diversity from Abundance Data}},
-url = {https://hal-agroparistech.archives-ouvertes.fr/hal-01212435},
-volume = {01212435},
-year = {2015}
-}
-@article{Amiti1999,
-author = {Amiti, Mary},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Amiti - 1999 - Specialization Patterns in Europe.pdf:pdf},
-journal = {Weltwirtschaftliches},
-number = {4},
-pages = {573--593},
-title = {{Specialization Patterns in Europe}},
-volume = {135},
-year = {1999}
-}
-@article{Smith1996,
-abstract = {Many indices have been proposed for measuring species evenness in ecological communities, but there is no consensus on which are best. We assemble criteria for an appropriate index for the evenness of a biological sample. The most important criterion is that evenness should be independent of species richness. Twelve previously proposed indices and variants are considered, and two apparently new indices. Four indices are recommended as joint best buys: A) If symmetry between minor and abundant species is not important, or if it is required that the index be less affected by minor species: 1) If it is essential that the index be able to reach a minimum of zero with any particular number of species, or if the shape of the index response to an evenness gradient is important: E(1/D) (based on a common form of Simpson's index). 2) If good mid-range behaviour is desired: E' (proposed by Camargo). B) If equal sensitivity to minor and abundant species is required: 1) If the shape of the index response to an evenness gradient is not important, the clear winner is: E(Q) (a new index). 2) If the shape Is Important: E(var) (another new index). The overall recommendation for general use is E(var).},
-annote = {Smith, B Wilson, JB},
-author = {Smith, B. and Wilson, J. Bastow},
-doi = {10.2307/3545749},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith, Wilson - 1996 - A consumer's guide to evenness indices.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {70--82},
-title = {{A consumer's guide to evenness indices}},
-url = {https://www.jstor.org/stable/3545749},
-volume = {76},
-year = {1996}
-}
-@article{Wright2006c,
-abstract = {Studies linking the functional diversity of a biota to ecosystem functioning typically employ a priori classifications of species into hypothetically complementary groups. However, multiple alternate classifications exist in which the number of functional groups, the number of species per functional group, and the grouping of species differ from the a priori scheme. Without assessing the relative precision, or ability of an a priori scheme to accurately predict ecosystem functioning relative to its many alternatives, the validity and utility of analyses based on a single a priori classification scheme remains unclear. We examine the precision of a priori classifications used in 10 experimental grassland systems in Europe and the United States that have found evidence for a significant role of functional plant diversity in governing ecosystem function. The predictive precision of the a priori classifications employed in these studies was seldom significantly higher than the precision of random classifications. Post-hoc classification schemes that performed well in predicting ecosystem function resembled each other more with regard to species composition than average classifications, but there was still considerable variability in the manner in which these classification schemes grouped species. These results suggest that we need a more nuanced understanding of how the diversity of functional traits of species in an assemblage affects ecosystem functioning.},
-author = {Wright, Justin P. and Naeem, Shahid and Hector, Andrew and Lehman, Clarence and Reich, Peter B. and Schmid, Bernhard and Tilman, David},
-doi = {10.1111/j.1461-0248.2005.00850.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2006 - Conventional functional classification schemes underestimate the relationship with ecosystem functioning.pdf:pdf},
-journal = {Ecology Letters},
-number = {2},
-pages = {111--120},
-title = {{Conventional functional classification schemes underestimate the relationship with ecosystem functioning}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2005.00850.x/abstract},
-volume = {9},
-year = {2006}
-}
-@article{Podani2013b,
-abstract = {A new approach to the measurement of functional diversity based on two-state nominal traits is developed from the florula diversity concept of P. Juh{\'{a}}sz-Nagy. For evaluating functional diversity of an assemblage, first a traits by species matrix is compiled. Various information theory functions are used to examine structural properties in this matrix, including the frequency distribution of trait combinations. The method is illustrated by actual examples, the first from plant communities prone to fire in Spain, and the second from running water invertebrate assemblages in Hungary. The results suggest that of the various functions used the standardized joint entropy, termed combinatorial functional evenness supplies most meaningful results. In plant communities, high fire recurrence decreased combinatorial functional evenness, while this measure for freshwater assemblages was uncorrelated with stream width and negatively correlated with the degree of human impact. Stream width is negatively correlated with the number of manifested functional combinations. In both case studies, combinatorial functional evenness has an inverse relationship to species richness - i.e., fewer species have a larger chance to produce equiprobable functional combinations.},
-annote = {Export Date: 12 March 2014
-Source: Scopus
-CODEN: CEOCA
-Language of Original Document: English
-Correspondence Address: Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, L. E{\"{o}}tv{\"{o}}s University, P{\'{a}}zm{\'{a}}ny P. s. 1/C, H-1117 Budapest, Hungary},
-author = {Podani, J{\'{a}}nos and Ricotta, Carlo and Pausas, J. G. and Schmera, D{\'{e}}nes},
-doi = {10.1556/ComEc.14.2013.2.8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani et al. - 2013 - Combinatorial functional diversity An information theoretical approach.pdf:pdf},
-journal = {Community Ecology},
-number = {2},
-pages = {180--188},
-title = {{Combinatorial functional diversity: An information theoretical approach}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84889666677{\&}partnerID=40{\&}md5=88f709883d7115e59d8620e1cc9dc2b9},
-volume = {14},
-year = {2013}
-}
-@article{Fuentes-Santos2017,
-abstract = {Comparing the spatial distribution of two spatial point patterns is an important issue in many scientific areas such as ecology, epidemiology or environmental risk assessment. However, up to date, the analysis of multitype point processes has been mainly focused on searching for interactions between events of different patterns, i.e. on the second-order structure, while the first-order structure has received less attention. This work proposes testing the similarity between two spatial point patterns through the comparison of their densities of event locations. For this purpose, we consider the usual squared discrepancy measure to propose a nonparametric statistical test. The asymptotic normal distribution of the associated statistic provides a calibration procedure. The simulation study conducted to analyze the performance of the test shows that this calibration can be too conservative and supports the use of a proposed bootstrap calibration. The performance of the test is also illustrated throughout its application to the analysis of the spatial patterns of wildfires registered in Galicia (NW Spain) during 2006.},
-author = {Fuentes-Santos, I. and Gonz{\'{a}}lez-Manteiga, W. and Mateu, Jorge},
-doi = {10.1016/j.spasta.2017.02.007},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fuentes-Santos, Gonz{\'{a}}lez-Manteiga, Mateu - 2017 - A nonparametric test for the comparison of first-order structures of spatial point pro.pdf:pdf},
-journal = {Spatial Statistics},
-title = {{A nonparametric test for the comparison of first-order structures of spatial point processes}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S2211675316301270},
-volume = {in press},
-year = {2017}
-}
-@article{Cornwell2006,
-abstract = {Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering. Key},
-author = {Cornwell, William K. and Schwilk, Dylan W. and Ackerly, David D.},
-doi = {10.1890/0012-9658(2006)87[1465:ATTFHF]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cornwell, Schwilk, Ackerly - 2006 - A trait-based test for habitat filtering Convex hull volume.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1465--1471},
-title = {{A trait-based test for habitat filtering: Convex hull volume}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2006)87[1465:ATTFHF]2.0.CO;2/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Grace2016,
-abstract = {How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis8, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.},
-author = {Grace, James B. and Anderson, T. Michael and Seabloom, Eric W. and Borer, Elizabeth T. and Adler, Peter B. and Harpole, W. Stanley and Hautier, Yann and Hillebrand, Helmut and Lind, Eric M. and P{\"{a}}rtel, Meelis and Bakker, Jonathan D. and Buckley, Yvonne M. and Crawley, Michael J. and Damschen, Ellen I. and Davies, Kendi F. and Fay, Philip A. and Firn, Jennifer and Gruner, Daniel S. and Hector, Andy and Knops, Johannes M. H. and MacDougall, Andrew S. and Melbourne, Brett A. and Morgan, John W. and Orrock, John L. and Prober, Suzanne M. and Smith, Melinda D.},
-doi = {10.1038/nature16524},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grace et al. - 2016 - Integrative modelling reveals mechanisms linking productivity and plant species richness.pdf:pdf},
-journal = {Nature},
-number = {7586},
-pages = {390--393},
-title = {{Integrative modelling reveals mechanisms linking productivity and plant species richness}},
-url = {http://www.nature.com/doifinder/10.1038/nature16524},
-volume = {529},
-year = {2016}
-}
-@incollection{Combes2004,
-address = {Amsterdam},
-author = {Combes, Pierre-Philippe and Overman, Henry G},
-booktitle = {Handbook of Urban and Regional Economics},
-chapter = {64},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Combes, Overman - 2004 - The spatial distribution of economic activities in the European Union(2).pdf:pdf},
-pages = {2845--2909},
-publisher = {Elsevier. North Holland},
-title = {{The spatial distribution of economic activities in the European Union}},
-volume = {4},
-year = {2004}
-}
-@article{Preisler1993,
-abstract = {Many species of bark-beetles kill trees in clusters. One of the most destructive forest insect pests with this colonization pattern is the mountain pine-beetle. Heavy losses caused by this beetle are of primary concern to national forest managers in western North America. An understanding of the process of tree selection by the beetles is useful for prescribing measures that might minimize beetle damage. Here, an autologistic model is used to study the spatial patterns of lodgepole pine trees attacked by the beetles. The model is used to describe the conditional probability that a tree of a given size, age and vigour is attacked given the status of all other trees in the stand. The spatial correlation between trees is modelled by constructing a covariate that is a measure of the angles from attacked trees to other trees in the stand. Some surprising difficulties in modelling conditional probabilities are discussed. Parameter estimates are obtained by maximizing a pseudolikelihood function, and estimates of standard errors are obtained from iteratively simulated samples.},
-author = {Preisler, Haiganoush K},
-doi = {10.2307/2986328},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Preisler - 1993 - Modelling Spatial Patterns of Trees Attacked by Bark-Beetles.pdf:pdf},
-journal = {Applied Statistics},
-number = {3},
-pages = {501--514},
-title = {{Modelling Spatial Patterns of Trees Attacked by Bark-Beetles}},
-volume = {42},
-year = {1993}
-}
-@article{Whitmore1996,
-abstract = {The growth of seedlings of ll species of Dipterocarpaceae in artificial canopy gaps of different sizes in a lowland evergreen dipterocarp rain forest in Sabah has been followed for 77 months. Three species were abundant and studied in most detail. The main objective was to analyse the foresters' observation, on which silviculture is based: as gap size increases, species that are more light-demanding win the race to fill the gap. Hopea nervosa seedlings had higher survival in closed forest than those of the other two well represented species, Parashorea malaanonan and Shoreajohorensis. From seedling demography these two species groups can be called shade-tolerants and light-demanders respectively. At 40 months the seedlings tallest at gap creation had increased their height advantage in all gap sizes. These were mainly H. nervosa. By 53 months, seedlings of Shoreajohorensis had grown ahead of H. nervosa in all but closed forest and tiny gaps of 6{\%} and 8{\%} canopy openness (I and 4 mol m- 2 day- 1 photosynthetically active radiation (p.a.r.) respectively). By 77 months they were even further ahead. Thus S. johorensis has a more flexible response. It is better able to use the extra p.a.r. of larger gaps (ca. 10{\%} openness or more; 10 mol m-2 day-1 p.a.r. or more), and is a light-demander in a second sense, whereas H. nervosa is light-indifferent in this sense. Seedlings of P. malaanonan unexpectedly failed to show rapid height growth in the larger gaps at 53 and 77 months. This species alone suffered very serious apical damage by herbivory. The II species under study occurred in various mixtures. To analyse success in gap-filling in the forest they were grouped by timber density into two classes. With increasing gap size, one group, six light hardwood species, known to be light-demanders, grow progressively ahead of the other group, four medium hardwood species, known to be shade-tolerant. P. malaanonan, also a light hardwood, grows only slowly because of herbivory. We find no evidence for fundamental niche differentiation. All species showed increasing rates of growth with increasing gap size. Species that responded more slowly might succeed in situations where they alone occur.},
-author = {Whitmore, T. C. and Brown, N. D.},
-doi = {10.1098/rstb.1996.0102},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whitmore, Brown - 1996 - Dipterocarp seedling growth in rain forest canopy gaps during six and a half years.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1344},
-pages = {1195--1203},
-title = {{Dipterocarp seedling growth in rain forest canopy gaps during six and a half years}},
-url = {http://rstb.royalsocietypublishing.org/content/351/1344/1195},
-volume = {351},
-year = {1996}
-}
-@article{Munoz2014,
-abstract = {Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k)is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I(k) in space and across taxonomic levels to test hypotheses about the ecological and evolutionary drivers of biodiversity patterns.},
-author = {Munoz, Fran{\c{c}}ois and Ramesh, B. R. and Couteron, Pierre},
-doi = {10.1890/13-0064.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Munoz, Ramesh, Couteron - 2014 - How do habitat filtering and niche conservatism affect community composition at different taxonomic res.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2179--2191},
-title = {{How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?}},
-url = {http://www.esajournals.org/doi/abs/10.1890/13-0064.1},
-volume = {95},
-year = {2014}
-}
-@book{Beguin1979,
-address = {Paris},
-author = {Beguin, Hubert},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beguin - 1979 - M{\'{e}}thodes d'Analyse G{\'{e}}ographique Quantitative.pdf:pdf},
-isbn = {2-7111-0193-2},
-pages = {1--282},
-publisher = {Librairies Techniques (LITEC)},
-title = {{M{\'{e}}thodes d'Analyse G{\'{e}}ographique Quantitative}},
-year = {1979}
-}
-@techreport{Haedo2012,
-abstract = {From data in the form of a two-way contingency table “Regions {\_} Sectors”, the concepts of specialization and concentration, built from the analysis of conditional distributions or profiles, is based on discrepancies among distributions: between profiles and a uniform distribution for absolute concepts; between profiles and the corresponding marginal distribution for the relative concepts; or between the joint distribution and the product of the marginal distributions for the global concept. This paper provides an extensive numerical analysis of measures derived from this approach and from other approaches used in the literature and shows that while the different measures under consideration display rather similar numerical behaviours, differences of ranking call for a particular care when interpreting the numerical results.},
-annote = {CORE Discussion Papers},
-author = {Haedo, Christian and Mouchart, Michel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haedo, Mouchart - 2012 - A stochastic independence approach for different measures of concentration and specialization.pdf:pdf},
-publisher = {Universit{\'{e}} catholique de Louvain, Center for Operations Research and Econometrics (CORE)},
-title = {{A stochastic independence approach for different measures of concentration and specialization}},
-url = {http://ideas.repec.org/p/cor/louvco/2012025.html},
-year = {2012}
-}
-@article{Gosselin2001,
-abstract = {Evenness is generally regarded as the constituent of species diversity which is independent of species richness. The group of most popular evenness indices has recently changed, following the influential work of Smith and Wilson (1996). My first point is to argue that this work failed to define coherently what evenness should be and thus advocated the use of indices of different nature. Instead, I propose to use the Lorenz partial order to choose indices that have a behaviour compatible with it. I then suggest a list of such evenness indices and build four series of . new. evenness indices. Finally, I discuss the interest of the Lorenz partial order and of the various evenness indices that are compatible with it.},
-author = {Gosselin, Fr{\'{e}}d{\'{e}}ric},
-doi = {10.1556/ComEc.2.2001.2.7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gosselin - 2001 - Lorenz partial order the best known logical framework to define evenness indices.pdf:pdf},
-journal = {Community Ecology},
-number = {2},
-pages = {197--207},
-title = {{Lorenz partial order: the best known logical framework to define evenness indices}},
-url = {http://dx.doi.org/10.1556/ComEc.2.2001.2.7},
-volume = {2},
-year = {2001}
-}
-@article{Huston1979,
-abstract = {Many explanations for diversity patterns have been proposed, and there have been several recent reviews of the subject (Pianka 1966, 1974; Ricklefs 1973; Pielou 1975). High diversity has been attributed both to intense competition which forces niche restriction (Dobzhansky 1950; MacArthur and Wilson 1967) and reduced competition resulting from predation (Paine 1966; Harper 1969;Janzen 1970; Connell 1975). Diversity has been positively correlated with productivity (Connell and Orias 1964; Pianka 1966; MacArthur 1969) and negatively correlated with productivity (Yount 1956; Margalef 1969). The question is far from settled. This paper develops an approach to the problem of species diversity based on the nonequilibrium interactions of competing populations. Under nonequilibrium conditions, differences in diversity are strongly influenced by variations in the rates of competitive displacement between communities, and such factors as relative competitive abilities, niche partitioning, etc., may not be particularly important. This approach deals primarily with the maintenance of diversity, as opposed to the generation of diversity. While most of the current diversity hypotheses have some relation to the evolutionary origin of diversity, this will not be emphasized here.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Huston, Michael},
-doi = {10.1086/283366},
-eprint = {arXiv:1011.1669v3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Huston - 1979 - A General Hypothesis of Species Diversity.pdf:pdf},
-isbn = {00030147},
-issn = {0003-0147},
-journal = {The American Naturalist},
-number = {1},
-pages = {81--101},
-pmid = {529},
-title = {{A General Hypothesis of Species Diversity}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/283366},
-volume = {113},
-year = {1979}
-}
-@article{Alsterberg2017,
-abstract = {Ecosystems worldwide are facing habitat homogenization due to human activities. Although it is commonly proposed that such habitat homogenization can have negative repercussions for ecosystem functioning, this question has yet to receive explicit scientific attention. We expand on the framework for evaluating the functional consequences of biodiversity loss by scaling up from the level of species to the level of the entire habitats. Just as species diversity generally fosters ecosystem functioning through positive interspecies interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and through exchange of material and energy across habitats. We show that experimental ecosystems comprised of a diversity of habitats show higher levels of multiple ecosystem functions than ecosystems with low habitat diversity. Our results demonstrate that the effect of habitat diversity on multifunctionality varies with season; it has direct effects on ecosystem functioning in summer and indirect effects, via changes in species diversity, in autumn, but no effect in spring. We propose that joint consideration of habitat diversity and species diversity will prove valuable for both environmental management and basic research.},
-author = {Alsterberg, Christian and Roger, Fabian and Sundb{\"{a}}ck, Kristina and Juhanson, Jaanis and Hulth, Stefan and Hallin, Sara and Gamfeldt, Lars},
-doi = {10.1126/sciadv.1601475},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alsterberg et al. - 2017 - Habitat diversity and ecosystem multifunctionality — The importance of direct and indirect effects.pdf:pdf},
-journal = {Science Advances},
-number = {2},
-pages = {e1601475},
-title = {{Habitat diversity and ecosystem multifunctionality — The importance of direct and indirect effects}},
-url = {http://advances.sciencemag.org/content/3/2/e1601475},
-volume = {3},
-year = {2017}
-}
-@book{Richards1952,
-abstract = {The rain forests of tropical America, Africa, Asia, and Australia are rapidly vanishing. With a focus on ecology, this book discusses rain forests as complex natural systems that are continually changing in response to climate and soil conditions, as well as to shifting cultivation, logging, and other human activities. The completely revised edition includes new chapters on climate (contributed by R.P.D. Walsh), microclimates and hydrology (contributed by R.P.D. Walsh), soils (contributed by I.C. Baillie) and an appendix on quantitative methods (contributed by P. Greig-Smith). This book, first published in 1952, is now a classic and represents an important record of what has become of the rain forest in the twentieth century and will be meaningful reading for botanists, ecologists, tropical biologists, conservationists, and general readers.},
-author = {Richards, P. W.},
-booktitle = {Cambridge Univ. Press, Cambridge, 450 pp},
-isbn = {0521421942},
-pages = {575},
-title = {{The tropical rain forest. An ecological study}},
-url = {https://books.google.com.my/books/about/The{\_}Tropical{\_}Rain{\_}Forest.html?id=43S-QgAACAAJ{\&}pgis=1},
-year = {1952}
-}
-@article{Aiginger2002,
-author = {Aiginger, Karl and Leitner, Wolfgang},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Aiginger, Leitner - 2002 - Regional concentration in the USA and Europe Who follows whom.pdf:pdf},
-journal = {Weltwirtschaftliches Archiv},
-number = {4},
-pages = {652--679},
-title = {{Regional concentration in the USA and Europe: Who follows whom?}},
-volume = {138},
-year = {2002}
-}
-@article{Duffy2003,
-abstract = {High plant species richness can enhance primary production, animal diversity, and invasion resistance. Yet theory predicts that plant and herbivore diversity, which often covary in nature, should have countervailing effects on ecosystem properties. Supporting this, we show in a seagrass system that increasing grazer diversity reduced both algal biomass and total community diversity, and facilitated dominance of a grazer-resistant invertebrate. In parallel with previous plant results, however, grazer diversity enhanced secondary production, a critical determinant of fish yield. Although sampling explained some diversity effects, only the most diverse grazer assemblage maximized multiple ecosystem properties simultaneously, producing a distinct ecosystem state. Importantly, ecosystem responses at high grazer diversity often differed in magnitude and sign from those predicted from summed impacts of individual species. Thus, complex interactions, often opposing plant diversity effects, arose as emergent consequences of changing consumer diversity, advising caution in extrapolating conclusions from plant diversity experiments to food webs.},
-author = {Duffy, J. Emmett and Richardson, J. Paul and Canuel, Elizabeth A.},
-doi = {10.1046/j.1461-0248.2003.00474.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duffy, Richardson, Canuel - 2003 - Grazer diversity effects on ecosystem functioning in seagrass beds.pdf:pdf},
-journal = {Ecology Letters},
-number = {7},
-pages = {637--645},
-title = {{Grazer diversity effects on ecosystem functioning in seagrass beds}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00474.x/abstract},
-volume = {6},
-year = {2003}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2009,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{Arr{\^{e}}t{\'{e}} du 28 ao{\^{u}}t 2009 pris pour l'application du d{\'{e}}cret n° 2002-634 du 29 avril 2002 modifi{\'{e}} portant cr{\'{e}}ation du compte {\'{e}}pargne-temps dans la fonction publique de l'Etat et dans la magistrature}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000021006687},
-year = {2009}
-}
-@article{Lawton1994,
-abstract = {Three aspects of the role of species in ecosystems are reviewed. (1) Theoretically, what are the possible relationships between ecosystem processes (Likens' (1992) 'trans- formation and flux of energy and matter') and the species richness of communities? (2) Summaries of two experiments with artificially constructed terrestrial ecosystems in the controlled environment facility known as the Ecotron are described. The first draws attention to the role of earthworms as 'ecosystem engineers'; the second explores changes in ecosystem processes in mesocosms assembled with three different levels of biological diversity. (3) Finally, a brief summary of the concept of organisms as ecosystem engineers is provided. The review is one of a growing number of publi- cations that attempt to break down the artificial and potentially damaging barriers that exist between ecosystem ecology and population biology. Loss of plant species may change and impair ecosystem processes under average environmental conditions, and reduce the ability of ecosystems to withstand, and recover from, extreme events. The very existence of some ecosystems depends on particular species - the major autogenic and allogenic engineers that create the system - and all ecosystems are probably modulated and modified to a significant extent by at least one species of engineer},
-author = {Lawton, John H.},
-doi = {10.2307/3545824},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lawton - 1994 - What do species do in ecosystems.pdf:pdf},
-journal = {Oikos},
-number = {3},
-pages = {367--374},
-title = {{What do species do in ecosystems?}},
-url = {https://www.jstor.org/stable/3545824},
-volume = {71},
-year = {1994}
-}
-@article{Zhang2009,
-abstract = {This paper establishes a necessary and sufficient condition for the asymptotic normality of the nonparametric estimator of sample coverage proposed by Good [Biometrica 40 (1953) 237-264]. This new necessary and sufficient condition extends the validity of the asymptotic normality beyond the previously proven cases.},
-annote = {ISI Document Delivery No.: 478RE
-Times Cited: 2
-Cited Reference Count: 20
-Zhang, Cun-Hui Zhang, Zhiyi
-Nsf [dms-05-04387, dms-06-04571, dms-08-04626]; nsa [mds 904-02-1-0063]
-Supported in part by NSF Grants DMS-05-04387, DMS-06-04571 and DMS-08-04626 and NSA Grant MDS 904-02-1-0063.
-Inst mathematical statistics
-Cleveland},
-author = {Zhang, Cun-Hui and Zhang, Zhiyi},
-doi = {10.1214/08-aos658},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Zhang - 2009 - Asymptotic Normality of a Nonparametric Estimator of Sample Coverage.pdf:pdf},
-journal = {Annals of Statistics},
-number = {5A},
-pages = {2582--2595},
-title = {{Asymptotic Normality of a Nonparametric Estimator of Sample Coverage}},
-volume = {37},
-year = {2009}
-}
-@article{Weitzman1992,
-author = {Weitzman, Martin L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weitzman - 1992 - On Diversity.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {2},
-pages = {363--405},
-title = {{On Diversity}},
-volume = {107},
-year = {1992}
-}
-@article{Grubb1977,
-abstract = {* 1According to ‘Gause's hypothesis' a corollary of the process of evolution by natural selection is that in a community at equilibrium every species must occupy a different niche. Many botanists have found this idea improbable because they have ignored the processes of regeneration in plant communities. * 2Most plant communities are longer-lived than their constituent individual plants. When an individual dies, it may or may not be replaced by an individual of the same species. It is this replacement stage which is all-important to the argument presented. * 3Several mechanisms not involving regeneration also contribute to the maintenance of species-richness: * (a).differences in life-form coupled with the inability of larger plants to exhaust or cut off all resources, also the development of dependence-relationships, * (b)differences in phenology coupled with tolerance of suppression, * (c)fluctuations in the environment coupled with relatively small differences in competitive ability between many species, * (d)the ability of certain species-pairs to form stable mixtures because of a balance of intraspecific competition against interspecific competition, * (e)the production of substances more toxic to the producer-species than to the other species, * (f)differences in the primary limiting mineral nutrients or pore-sizes in the soil for neighbouring plants of different soecies, and * (g)differences in the competitive abilities of species dependent on their physiological age coupled with the uneven-age structure of many populations. * 4The mechanisms listed above do not go far to explain the indefinite persistence in mixture of the many species in the most species-rich communities known. * 5In contrast there seem to be almost limitless possibilities for differences between species in their requirements for regeneration, i.e. the replacement of the individual plants of one generation by those of the next. This idea is illustrated for tree species and it is emphasized that foresters were the first by a wide margin to appreciate its importance. * 6The processes involved in the successful invasion of a gap by a given plant species and some characters of the gap that may be important are summarized in Table 2. * 7The definition of a plant's niche requires recognition of four components: * (a)the habitat niche, * (b)the life-form niche, * (c)the phenological niche, and * (d)the regeneration niche. * 8A brief account is given of the patterns of regeneration in different kinds of plant community to provide a background for studies of differentiation in the regeneration niche. * 9All stages in the regeneration-cycle are potentially important and examples of differentiation between species are given for each of the following stages: * (a)Production of viable seed (including the sub-stages of flowering, pollination and seed-set), * (b)dispersal, in space and time, * (c)germination, * (d)establishment, and * (e)further development of the immature plant. * 10In the concluding discussion emphasis is placed on the following themes: * (a)the kinds of work needed in future to prove or disprove that differentiation in the regeneration niche is the major explanation of the maintenance of species-richness in plant communities, * (b)the relation of the present thesis to published ideas on the origin of phenological spread, * (c)the relevance of the present thesis to the discussion on the presence of continua in vegetation, * (d)the co-incidence of the present thesis and the emerging ideas of evolutionists about differentiation of angiosperm taxa, and * (e)the importance of regeneration-studies for conservation.},
-author = {Grubb, P J},
-doi = {10.1111/j.1469-185X.1977.tb01347.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grubb - 1977 - the Maintenance of Species-Richness in Plant Communities the Importance of the Regeneration Niche.pdf:pdf},
-isbn = {1469-185X},
-issn = {1464-7931},
-journal = {Biological Reviews},
-number = {1},
-pages = {107--145},
-pmid = {365},
-title = {{the Maintenance of Species-Richness in Plant Communities: the Importance of the Regeneration Niche}},
-url = {http://dx.doi.org/10.1111/j.1469-185X.1977.tb01347.x{\%}5Cnhttp://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.1977.tb01347.x/abstract},
-volume = {52},
-year = {1977}
-}
-@article{Cox1955,
-abstract = {The paper deals with a number of problems of statistical analysis connected with events occurring haphazardly in space or time. The topics discussed include: tests of randomness, components of variance, the correlation between events of different types, and a modification of the snap-round method used in operational research.},
-author = {Cox, D. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cox - 1955 - Some Statistical Methods Connected with Series of Events.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {129--164},
-title = {{Some Statistical Methods Connected with Series of Events}},
-url = {https://www.jstor.org/stable/2983950},
-volume = {17},
-year = {1955}
-}
-@article{Baker2014,
-abstract = {The Amazon rain forest sustains the world's highest tree diversity, but it remains unclear why some clades of trees are hyperdiverse, whereas others are not. Using dated phylogenies, estimates of current species richness and trait and demographic data from a large network of forest plots, we show that fast demographic traits--short turnover times--are associated with high diversification rates across 51 clades of canopy trees. This relationship is robust to assuming that diversification rates are either constant or decline over time, and occurs in a wide range of Neotropical tree lineages. This finding reveals the crucial role of intrinsic, ecological variation among clades for understanding the origin of the remarkable diversity of Amazonian trees and forests.},
-author = {Baker, Timothy R. and Pennington, R. Toby and Magallon, Susana and Gloor, Emanuel and Laurance, William F. and Alexiades, Miguel N. and Alvarez, Esteban and Araujo, Alejandro and Arets, Eric J. M. M. and Aymard, Gerardo A. and de Oliveira, Atila Alves and Amaral, I{\^{e}}da Le{\~{a}}o and Arroyo, Luzmila and Bonal, Damien and Brienen, Roel J. W. and Chave, J{\'{e}}r{\^{o}}me and Dexter, Kyle G. and {Di Fiore}, Anthony and Eler, Eduardo and Feldpausch, Ted R. and Ferreira, Leandro and Lopez-Gonzalez, Gabriela and van der Heijden, Geertje and Higuchi, Niro and Honorio, Eur{\'{i}}dice and Huamantupa, Isau and Killeen, Tim J. and Laurance, Susan and Lea{\~{n}}o, Claudio and Lewis, Simon L. and Malhi, Yadvinder and Marimon, Beatriz Schwantes and {Marimon Junior}, Ben Hur and {Monteagudo Mendoza}, Abel and Neill, David and Pe{\~{n}}uela-Mora, Maria Cristina and Pitman, Nigel and Prieto, Adriana and Quesada, Carlos A. and Ram{\'{i}}rez, Fredy and {Ram{\'{i}}rez Angulo}, Hirma and Rudas, Agustin and Ruschel, Ademir R. and Salom{\~{a}}o, Rafael P. and de Andrade, Ana Segalin and Silva, J. Natalino M. and Silveira, Marcos and Simon, Marcelo F. and Spironello, Wilson and Steege, Hans Ter and Terborgh, John and Toledo, Marisol and Torres-Lezama, Armando and Vasquez, Rodolfo and Vieira, Ima C{\'{e}}lia Guimar{\~{a}}es and Vilanova, Emilio and Vos, Vincent A. and Phillips, Oliver L.},
-doi = {10.1111/ele.12252},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baker et al. - 2014 - Fast demographic traits promote high diversification rates of Amazonian trees.pdf:pdf},
-journal = {Ecology Letters},
-pages = {527--536},
-title = {{Fast demographic traits promote high diversification rates of Amazonian trees}},
-volume = {17},
-year = {2014}
-}
-@article{Fattorini1999,
-abstract = {The use of intrinsic diversity profiles is recommended for ranking biological populations according to their diversity. The profiles are estimated on the basis of independent replications of a suitable sampling design. Asymptotically conservative joint confidence bands are constructed by the Richmond method, while equivalence hypotheses of couples of profiles are assessed against dominance or crossing alternatives by a multiple comparison test. The proposed procedures are applied for obtaining a partial diversity ordering for the avian populations settled in some selected parks in the north of Italy.},
-author = {Fattorini, L. and Marcheselli, M.},
-doi = {10.1002/(SICI)1099-095X(199909/10)10:5<589::AID-ENV374>3.0.CO;2-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fattorini, Marcheselli - 1999 - Inference on intrinsic diversity profiles of biological populations.pdf:pdf},
-issn = {11804009},
-journal = {Environmetrics},
-number = {5},
-pages = {589--599},
-title = {{Inference on intrinsic diversity profiles of biological populations}},
-volume = {10},
-year = {1999}
-}
-@article{Brummitt2016,
-abstract = {In 2013, the Group on Earth Observations Biodiversity Observation Network (GEO BON) developed the framework of Essential Biodiversity Variables (EBVs), inspired by the Essential Climate Variables (ECVs). The EBV framework was developed to distill the complexity of biodiversity into a manageable list of priorities and to bring a more coordinated approach to observing biodiversity on a global scale. However, efforts to address the scientific challenges associated with this task have been hindered by diverse interpretations of the definition of an EBV. Here, the authors define an EBV as a critical biological variable that characterizes an aspect of biodiversity, functioning as the interface between raw data and indicators. This relationship is clarified through a multi-faceted stock market analogy, drawing from relevant examples of biodiversity indicators that use EBVs, such as the Living Planet Index and the UK Spring Index. Through this analogy, the authors seek to make the EBV concept accessible to a wider audience, especially to non-specialists and those in the policy sector, and to more clearly define the roles of EBVs and their relationship with biodiversity indicators. From this we expect to support advancement towards globally coordinated measurements of biodiversity.},
-author = {Brummitt, Neil and Regan, Eugenie C. and Weatherdon, Lauren V. and Martin, Corinne S. and Geijzendorffer, Ilse R. and Rocchini, Duccio and Gavish, Yoni and Haase, Peter and Marsh, Charles J. and Schmeller, Dirk S.},
-doi = {10.1016/j.biocon.2016.09.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brummitt et al. - 2016 - Taking stock of nature Essential biodiversity variables explained.pdf:pdf},
-journal = {Biological Conservation},
-title = {{Taking stock of nature : Essential biodiversity variables explained}},
-url = {http://dx.doi.org/10.1016/j.biocon.2016.09.006},
-volume = {in press},
-year = {2016}
-}
-@article{Bar-Hen2015,
-abstract = {Motivated by the analysis of the impact of ecological processes on spatial distribution of tree species, we introduce in this paper a novel approach to detect spatial cluster of points. Our procedure is based on an iterative transformation of the distance between points into a measure of closeness. Our measure has the advantage of being independent of an arbitrary cluster shape and allowing adjustment for covariates. The comparison of the observed measure of closeness to a reference point process leads to a hierarchical clustering of spatial points. The selection of the optimal number of clusters is performed using the Gap statistic. Our procedure is illustrated on a spatial distribution of the Dicorynia guianensis species in the French Guiana terra firme rainforest.},
-author = {Bar-Hen, Avner and Emily, Mathieu and Picard, Nicolas},
-doi = {10.1016/j.spasta.2015.07.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bar-Hen, Emily, Picard - 2015 - Spatial cluster detection using nearest neighbor distance.pdf:pdf},
-journal = {Spatial Statistics},
-number = {C},
-pages = {400--411},
-title = {{Spatial cluster detection using nearest neighbor distance}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S221167531500069X},
-volume = {14},
-year = {2015}
-}
-@article{Banasek-Richter2004,
-abstract = {Food-web descriptors serve as a means for among-web comparisons that are necessary for the discovery of regularities in respect to food-web structure. Qualitative descriptors were however found to be highly sensitive to varying levels of sampling effort. To circumvent these shortcomings, quantitative counterparts were proposed which take the magnitude of trophic interaction between species into consideration. For 14 properties we examined the performance with increasing sampling effort of a qualitative, an unweighted quantitative (giving the same weight to each taxon), and a weighted quantitative version (weighing each taxon by the amount of incoming and outgoing flows). The evaluation of 10 extensively documented quantitative webs formed the basis for this analysis. The quantitative versions were found to be much more robust against variable sampling effort. This increase in accuracy is accomplished at the cost of a slight decrease in precision as compared to the qualitative properties. Conversely, the quantitative descriptors also proved less sensitive to differences in evenness in the distribution of link magnitude. By more adequately incorporating the information inherent to quantitative food-web compilations, quantitative descriptors are able to better represent the web, and are thus more suitable for the elucidation of general trends in food-web structure. {\textcopyright} 2003 Elsevier Ltd. All rights reserved.},
-author = {Bana{\v{s}}ek-Richter, Carolin and Cattin, Marie-France and Bersier, Louis-F{\'{e}}lix},
-doi = {10.1016/S0022-5193(03)00305-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bana{\v{s}}ek-Richter, Cattin, Bersier - 2004 - Sampling effects and the robustness of quantitative and qualitative food-web descriptors.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {1},
-pages = {23--32},
-title = {{Sampling effects and the robustness of quantitative and qualitative food-web descriptors}},
-volume = {226},
-year = {2004}
-}
-@article{Leinster2009,
-abstract = {This is a preliminary article stating and proving a new maximum entropy theorem. The entropies that we consider can be used as measures of biodiversity. In that context, the question is: for a given collection of species, which frequency distribution(s) maximize the diversity? The theorem provides the answer. The chief surprise is that although we are dealing with not just a single entropy, but a one-parameter family of entropies, there is a single distribution maximizing all of them simultaneously.},
-archivePrefix = {arXiv},
-arxivId = {0910.0906},
-author = {Leinster, Tom},
-eprint = {0910.0906},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leinster - 2009 - A maximum entropy theorem with applications to the measurement of biodiversity.pdf:pdf},
-journal = {arXiv},
-number = {v4},
-title = {{A maximum entropy theorem with applications to the measurement of biodiversity}},
-url = {http://arxiv.org/abs/0910.0906v4},
-volume = {0910.0906},
-year = {2009}
-}
-@article{Preston1960,
-author = {Preston, F. W.},
-doi = {10.2307/1931793},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Preston - 1960 - Time and Space and the Variation of Species.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {611--627},
-title = {{Time and Space and the Variation of Species}},
-url = {http://dx.doi.org/10.2307/1931793},
-volume = {41},
-year = {1960}
-}
-@article{Saito2016,
-abstract = {The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of $\alpha$ and $\beta$ niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while $\alpha$ niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co-occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.},
-author = {Saito, Victor S. and Cianciaruso, Marcus Vinicius and Siqueira, Tadeu and Fonseca-Gessner, Alaide A. and Pavoine, Sandrine},
-doi = {10.1002/ece3.2081},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Saito et al. - 2016 - Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect.pdf:pdf},
-journal = {Ecology and Evolution},
-number = {9},
-pages = {2925--2937},
-title = {{Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities}},
-url = {http://doi.wiley.com/10.1002/ece3.2081},
-volume = {6},
-year = {2016}
-}
-@article{Ricotta2008,
-abstract = {The utility of biodiversity measures that incorporate pairwise species functional differences is becoming increasingly recognized. Functional diversity is regarded as the key for linking community composition to ecosystem processes like productivity, nutrient cycling, carbon sequestration, or stability when subject to perturbations. Therefore, several indices have been proposed to measure the functional diversity of a given species assemblage. The principle behind these measures is that a species assemblage with high functional overlap among species has a lower functional diversity than an assemblage with low functional overlap. On the other hand, the variability in the species functional characters among different species assemblages (i.e., functional beta diversity) has received much less attention. The aim of this paper is thus to discuss a general framework for calculating functional beta diversity from plot-to-plot functional dissimilarity matrices. To illustrate our proposal we use data from two beech forest stands with different management histories in central Italy. The results of our analysis show that, though the two stands are significantly different from one another in terms of their species functional traits, the difference in their functional beta diversity values is only marginally significant. These results are related to the characteristic scale at which ecological variations occur in the two stands.},
-annote = {Cited By (since 1996):18
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniromal.it},
-author = {Ricotta, Carlo and Burrascano, Sabina},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Burrascano - 2008 - Beta diversity for functional ecology.pdf:pdf},
-journal = {Preslia},
-number = {1},
-pages = {61--72},
-title = {{Beta diversity for functional ecology}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-44649149179{\&}partnerID=40{\&}md5=2098c0113ec829f76233ca1d0fb94083},
-volume = {80},
-year = {2008}
-}
-@article{Smith2012,
-abstract = {Question How are heterogeneitydiversity relationships (HDRs) influenced by spatial structure in environmental variables, sampling grain and the extent of niche differentiation? Methods We developed a spatially explicit simulation model incorporating variable dispersal distances and competition strength on fractal landscapes. By varying the grain used to sample these models, we examined scaling patterns in HDR metrics at fine scales (sampling grain from 100 to 10 000 individuals, sampling extent ca. 260 000 individuals). Results Environmental geometry exerts an important influence on the ecological processes responsible for HDRs. Unique geometric characteristics of individual landscapes can greatly influence emergent community properties; field studies frequently use inadequate sample sizes to account for this phenomenon. Two opposing processes influence spatial scaling of HDRs: variance partitioning, which favours smaller-grained samples, and mass effects, which favour larger-grained samples. In assessing HDRs, diversity is more sensitive than species richness, and should be the preferred measure in field studies. The environmental geometry and age of a community interact: compared to high fractal dimension landscapes, low fractal dimension landscapes are slower to develop HDRs, but in the long term their HDRs will be higher. Conclusions Our study demonstrates that, despite the superficial simplicity of the concept, HDRs vary in complex and non-intuitive ways, and warrant further theoretical and empirical study. More generally, environmental geometry is likely to exert a strong influence on many emergent community processes, but we do not yet have a firm understanding of this relationship.},
-annote = {ISI Document Delivery No.: 968EJ
-Times Cited: 0
-Cited Reference Count: 44
-Smith, Tyler W. Lundholm, Jeremy T.
-Natural Sciences and Engineering Research Council of Canada (NSERC); NSERC
-Michael Palmer provided helpful comments on an earlier draft of this paper, and shared some of the code used to develop his original simulation models (Palmer 1992). Additional comments were provided by two anonymous reviewers. Funding for this study was provided by a Natural Sciences and Engineering Research Council of Canada (NSERC) grant to JTL and an NSERC postdoctoral fellowship to TWS. Computing resources were provided by the Atlantic Computational Excellence network (ACEnet).
-Wiley-blackwell
-Hoboken},
-author = {Smith, T. W. and Lundholm, J. T.},
-doi = {10.1111/j.1654-1103.2011.01380.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith, Lundholm - 2012 - Environmental geometry and heterogeneity-diversity relationships in spatially explicit simulated communities.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {732--744},
-title = {{Environmental geometry and heterogeneity-diversity relationships in spatially explicit simulated communities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2011.01380.x/full},
-volume = {23},
-year = {2012}
-}
-@article{Beatty1984,
-abstract = {In a maple-beech forest in eastern New York, equal numbers of mounds, pits, and adjacent undisturbed soil microsites were caused for plant species density and cover over the growing seasons of 1978 and 1979. Several soil properties were also measured for each microsite. Detrended correspondence analysis (DCA) and chi-square goodness-of-fit tests were used to test whether the species were uniformly distributed over the microrelief positions. Comparisons of species composition, diversity, and vegetative phenologies were made between microsites and between hemlock- and hardwood-dominated forest areas. Differences in soil properties between microsites and between the two forest areas were assessed with one-tailed paried t test and Wilcoxon rank-sum tests, respectively. Microrelief created a mosaic of soil properties and a vegetation pattern in the understory, both of which were affected by the presence of hemlock in the canopy. Ordinations (DCA) indicated two factors that affected species compostion of the microsites: (1) presence of hemlock (Tsuga canadensis) as the nearest canopy tree, and (2) microtopography (whether the microsite was a mound, pit, or undisturbed-soil site). Species in non-hemlock areas had patchy distributions in the forest community: eight species grew mainly on mounds, six in pits, and five on undisturbed soil. The mounds and pits had characteristic assemblages of species. Species richness and total density and cover of plants in each microsite were constant over the growing season. In contrast, little spatial or temporal community pattern was apparent in forest areas influenced by hemlock. The effect of hemlock on species distributions was due in part to its effect on soil properties. For all microsites, forest areas with hemlock had greater soil organic matter content, available nitrogen, cation exchange capacity, and little depth, lower soil calcium content, moisture content, temperature, pH, and A"1 horizon depth; and no frost heaving. Microrelief also affected soil properties significantly. In comparison with pits, mounds were drier and poorer in nutrient content, and had a lower cation exchange capacity, less organic matter, less little cover, a thinner A"1 horizon, and less snow accumulation. In areas without hemlock, the mounds were also more acid, warmer in summer and colder in winter, and more subject to frost heaving than pits. Hemlock-influenced areas had no consistent microsite differences in pH or temperature. The different microenvirnments, created by the interaction of microrelief and hemlock, resulted in patchy distributions of most understory species. This pattern was likely a reuslt of species requirements for and tolerances of envirnomental conditions, tempered by competitive interactions.},
-author = {Beatty, Susan W.},
-doi = {10.2307/1939121},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beatty - 1984 - Influence of microtopography and canopy species on spatial patterns of forest understorey plants.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {1406--1419},
-title = {{Influence of microtopography and canopy species on spatial patterns of forest understorey plants}},
-url = {http://www.jstor.org/stable/1939121},
-volume = {65},
-year = {1984}
-}
-@article{Leimu2005,
-abstract = {Citation frequencies of scientific articles are increasingly used for academic evaluation in various disciplines, including ecology. However, the factors affecting cita- tion rates have not been extensively studied. Here, we examine the association between the citation frequency of ecological articles and various characteristics of journals, articles and authors. Our analysis shows that the annual citation rates of ecological papers are affected by the direction of the study outcome with respect to the hypothesis tested (supportive versus unsupportive evidence), by article length, by the number of authors, and by their country and university of affiliation. These results cast doubt on the validity of using citation counts as an objective and unbiased tool for academic evaluation in ecology.},
-annote = {TY - JOUR},
-author = {Leimu, Roosa and Koricheva, Julia},
-doi = {10.1016/j.tree.2004.10.010},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leimu, Koricheva - 2005 - What determines the citation frequency of ecological papers.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {1},
-pages = {28--32},
-title = {{What determines the citation frequency of ecological papers?}},
-url = {http://www.sciencedirect.com/science/article/B6VJ1-4DTP2WP-1/2/c8a9a48e8c426c25d8408c0c52f1d6e8},
-volume = {20},
-year = {2005}
-}
-@article{Jaccard1901,
-abstract = {Jaccard, Paul (1901), "{\'{E}}tude comparative de la distribution florale dans une portion des Alpes et des Jura", Bulletin de la Soci{\'{e}}t{\'{e}} Vaudoise des Sciences Naturelles 37: 547–579.},
-author = {Jaccard, Paul},
-doi = {http://dx.doi.org/10.5169/seals-266450},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaccard - 1901 - {\'{E}}tude comparative de la distribution florale dans une portion des Alpes et du Jura.pdf:pdf},
-journal = {Bulletin de la Soci{\'{e}}t{\'{e}} Vaudoise des Sciences Naturelles},
-pages = {547--579},
-title = {{{\'{E}}tude comparative de la distribution florale dans une portion des Alpes et du Jura}},
-volume = {37},
-year = {1901}
-}
-@article{Borland1998,
-abstract = {We discuss the information theoretical foundations of the Kullback information gain, recently generalized within a nonextensive thermostatistical formalism. General properties are studied and, in particular, a consistent test for measuring the degree of correlation between random variables is proposed. In addition, minimum entropy distributions are discussed and the H-theorem is proved within the generalized context.},
-author = {Borland, Lisa and Plastino, Angel R. and Tsallis, Constantino},
-doi = {10.1063/1.532660},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borland, Plastino, Tsallis - 1998 - Information gain within nonextensive thermostatistics.pdf:pdf},
-journal = {Journal of Mathematical Physics},
-number = {12},
-pages = {6490--6501},
-title = {{Information gain within nonextensive thermostatistics}},
-url = {http://dx.doi.org/10.1063/1.532660},
-volume = {39},
-year = {1998}
-}
-@misc{Cirad2010,
-address = {Montpellier},
-author = {{Cirad - D{\'{e}}l{\'{e}}gation {\`{a}} l'Information Scientifique et Technique}},
-title = {{Guide de la profession d'auteur au Cirad}},
-url = {http://intranet-dist.cirad.fr/content/download/885/7105/file/Note-diffusion-guide-profession-auteur-EH-janvier-2010.pdf},
-year = {2010}
-}
-@techreport{Conceicao2000,
-address = {Austin, Texas},
-author = {Concei{\c{c}}{\~{a}}o, Pedro and Ferreira, Pedro},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Concei{\c{c}}{\~{a}}o, Ferreira - 2000 - The Young Person's Guide to the Theil Index Suggesting Intuitive Interpretations and Exploring Analytical A.pdf:pdf},
-pages = {54},
-title = {{The Young Person's Guide to the Theil Index: Suggesting Intuitive Interpretations and Exploring Analytical Applications}},
-url = {http://ssrn.com/paper=228703},
-year = {2000}
-}
-@article{Feller1943,
-author = {Feller, W},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feller - 1943 - On a general class of contagious distributions.pdf:pdf},
-journal = {The Annals of Mathematical Statistics},
-number = {4},
-pages = {389--400},
-title = {{On a general class of contagious distributions}},
-url = {https://www.jstor.org/stable/2235926},
-volume = {14},
-year = {1943}
-}
-@article{Mori1994,
-abstract = {An analysis of the flowering plant flora of a lowland moist forest in central French Guiana reveals 298 species with adaptations for wind dispersal. This represents 16.2{\%} of the flowering plant flora and 9.8{\%} of the class Magnoliopsida (dicotyledons). The most diverse wind-dispersed families are the Orchidaceae in the Liliopsida (monocotyledons) with 135 species and the Bignoniaceae in the Magnoliopsida with 37 species. The wind-dispersed species of central French Guiana have evolved either small, dust-like seeds, fruits or seeds with various kinds or wings, fruits or seeds with tufts of hairs, or expanded wing-or parachute like persistent calyces. Most wind-dispersed species, among the liliopsids, are epiphytes and, among the magnoliopsids, trees or lianas. In central French Guiana, collections of these species with mature diaspores have been gathered most often in October and March, the months with peak wind velocities. In contrast, collections from June and July, when wind velocities are at a minimum, are rare. CR - Copyright {\&}169; 1994 New York Botanical Garden Press},
-author = {Mori, Scott A. and Brown, John L.},
-doi = {10.2307/2807152},
-journal = {Brittonia},
-number = {2},
-pages = {105},
-title = {{Report on Wind Dispersal in a Lowland Moist Forest in Central French Guiana}},
-volume = {46},
-year = {1994}
-}
-@article{Wilkinson1999,
-author = {Wilkinson, David M.},
-doi = {10.2307/3546874},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilkinson - 1999 - The disturbing history of intermediate disturbance.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {145--147},
-title = {{The disturbing history of intermediate disturbance}},
-url = {http://www.jstor.org/stable/3546874},
-volume = {84},
-year = {1999}
-}
-@article{Kahmen2005,
-abstract = {In the past years, a number of studies have used experimental plant communities to test if biodiversity influences ecosystem functioning such as productivity. It has been argued, however, that the results achieved in experimental studies may have little predictive value for species loss in natural ecosystems. Studies in natural ecosystems have been equivocal, mainly because in natural ecosystems differences in diversity are often confounded with differences in land use history or abiotic parameters. In this study, we investigated the effect of plant diversity on ecosystem functioning in semi-natural grasslands. In an area of 10 x 20 km, we selected 78 sites and tested the effects of various measures of diversity and plant community composition on productivity. We separated the effects of plant diversity on ecosystem functioning from potentially confounding effects of community composition, management or environmental parameters, using multivariate statistical analyses. In the investigated grasslands, simple measures of biodiversity were insignificant predictors of productivity. However, plant community composition explained productivity very well (R-2=0.31) and was a better predictor than environmental variables (soil and site characteristics) or management regime. Thus, complex measures such as community composition and structure are important drivers for ecosystem functions in semi-natural grasslands. Furthermore, our data show that it is difficult to extrapolate results from experimental studies to semi-natural ecosystems, although there is a need to investigate natural ecosystems to fully understand the relationship of biodiversity and ecosystem functioning.},
-author = {Kahmen, Ansgar and Perner, J{\"{o}}rg and Audorff, Volker and Weisser, Wolfgang and Buchmann, Nina},
-doi = {10.1007/s00442-004-1749-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kahmen et al. - 2005 - Effects of plant diversity, community composition and environmental parameters on productivity in montane Europea.pdf:pdf},
-journal = {Oecologia},
-number = {4},
-pages = {606--615},
-title = {{Effects of plant diversity, community composition and environmental parameters on productivity in montane European grasslands}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs00442-004-1749-2},
-volume = {142},
-year = {2005}
-}
-@article{Engen1977,
-author = {Engen, Steinar},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Engen - 1977 - Exponential and Logarithmic Species-Area Curves.pdf:pdf},
-journal = {The American Naturalist},
-number = {979},
-pages = {591--594},
-title = {{Exponential and Logarithmic Species-Area Curves}},
-url = {http://www.jstor.org/stable/2460244},
-volume = {111},
-year = {1977}
-}
-@article{Guan2008b,
-abstract = {We propose a formal method to test stationarity for spatial point processes. The proposed test statistic is based on the integrated squared deviations of observed counts of events from their means estimated under stationarity. We show that the resulting test statistic converges in distribution to a functional of a two-dimensional Brownian motion. To conduct the test, we compare the calculated statistic with the upper tail critical values of this functional. Our method requires only a weak dependence condition on the process but does not assume any parametric model for it. As a result, it can be applied to a wide class of spatial point process models. We study the efficacy of the test through both simulations and applications to two real data examples that were previously suspected to be nonstationary based on graphical evidence. Our test formally confirmed the suspected nonstationarity for both data.},
-annote = {cited By (since 1996) 0},
-author = {Guan, Yontao},
-doi = {10.1111/j.1541-0420.2007.00977.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2008 - A KPSS test for stationarity for spatial point processes.pdf:pdf},
-journal = {Biometrics},
-number = {3},
-pages = {800--806},
-title = {{A KPSS test for stationarity for spatial point processes}},
-volume = {64},
-year = {2008}
-}
-@article{Pagel1997,
-abstract = {Evolutionary processes shape the regular trends of evolution and are responsible for the diversity and distribution of contemporary species. They include correlated evolutionary change and trajectories of trait evolution, convergent and parallel evolution, differential rates of evolution, speciation and extinction, the order and direction of change in characters, and the nature of the evolutionary process itself—does change accumulate gradually, episodically, or in punctuational bursts. Phylogenies, in combination with information on species, contain the imprint of these historical evolutionary processes. By applying comparative methods based upon statistical models of evolution to well resolved phylogenies, it is possible to infer the historical evolutionary processes that must have existed in the past, given the patterns of diversity seen in the present. I describe a set of maximum likelihood statistical methods for inferring such processes. The methods estimate parameters of statistical models for inferring correlated evolutionary change in continuously varying characters, for detecting correlated evolution in discrete characters, for estimating rates of evolution, and for investigating the nature of the evolutionary process itself. They also anticipate the wealth of information becoming available to biological scientists from genetic studies that pin down relationships among organisms with unprecedented accuracy.},
-author = {Pagel, Mark},
-doi = {10.1111/j.1463-6409.1997.tb00423.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pagel - 1997 - Inferring evolutionary processes from phylogenies.pdf:pdf},
-journal = {Zoologica Scripta},
-number = {4},
-pages = {331--348},
-title = {{Inferring evolutionary processes from phylogenies}},
-url = {http://dx.doi.org/10.1111/j.1463-6409.1997.tb00423.x},
-volume = {26},
-year = {1997}
-}
-@article{Kosman2003,
-abstract = {It has been established that Nei's measure of the average genetic diversity per locus, H S , and the measure of average differences between isolates with respect to simple mismatch dissimilarity, are identical measures of diversity within populations. The M{\"{u}}ller index of diversity can be considered as the correction of Nei's measure for small samples.},
-author = {Kosman, Evsey},
-doi = {10.1046/j.1365-3059.2003.00923.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosman - 2003 - Nei's gene diversity and the index of average differences are identical measures of diversity within populations.pdf:pdf},
-journal = {Plant Pathology},
-number = {5},
-pages = {533--535},
-title = {{Nei's gene diversity and the index of average differences are identical measures of diversity within populations}},
-url = {http://doi.wiley.com/10.1046/j.1365-3059.2003.00923.x},
-volume = {52},
-year = {2003}
-}
-@article{Podani2016,
-abstract = {Presence–absence based beta diversity defined for pairs of sites may be partitioned into components following two different ways of thinking. Within the framework of Baselga (abbreviated hereafter as BAS), nestedness is crucial and dissimilarity is partitioned into replacement (turnover) and nestedness-resultant fractions. The method proposed by Podani and Schmera (POD), however, places emphasis on the mathematical additivity of components and divides dissimilarity into replacement and richness difference components. A recent compari- son by Baselga and Leprieur (2015), on the example of the Jaccard family of indices, emphasizes the indepen- dence of replacement component from absolute richness difference and concludes that the replacement function of the BAS framework is the only true measure of species replacement. As a response to this study, we show here that 1) the sacrifice one must make for independence is that the components themselves are scaled differently and are not always comparable ecologically, 2) absolute (raw) replacement and richness differ- ence are not independent, so that independence fromthe latter cannot be a fundamental criterion that a replace- mentmeasure should satisfy, 3) relativization applied in thePODframework is ecologically interpretable, leading to ameaningful conceptualization of species replacement, 4) theBAS andPODmethods are linked through a gen- eralized replacement function, 5) both theBASand PODapproachesmay produce highcorrelationswithenviron- mental variables,whereas 6) the PODapproach offers inmany respectsmore illuminating demonstrations of the underlying changes of pattern than the graphs of Baselga and Leprieur for both artificial and actual fish distribu- tion data. {\textcopyright}},
-author = {Podani, J{\'{a}}nos and Schmera, D{\'{e}}nes},
-doi = {10.1016/j.ecoinf.2016.01.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani, Schmera - 2016 - Once again on the components of pairwise beta diversity.pdf:pdf},
-journal = {Ecological Informatics},
-pages = {63--68},
-title = {{Once again on the components of pairwise beta diversity}},
-url = {http://dx.doi.org/10.1016/j.ecoinf.2016.01.002},
-volume = {32},
-year = {2016}
-}
-@article{Richard-Hansen2015,
-abstract = {Whereasbroad-scaleAmazonianforest typeshave beenshownto influence the structure of the communities of medium- to large-bodied vertebrates, their natural heterogeneity at smaller scale or within the terra firme forests remains poorly described and understood. Diversity indices of such communities and the relative abundance of the 21 most commonly observed species were compared from standardized line-transect data across 25 study sites distributed in undisturbed forests in French Guiana.We first assessed the relevance of a forest typology based on geomorphological landscapes to explain the observed heterogeneity. As previously found for tree beta-diversity patterns, this new typology proved to be a non-negligible factor underlying the beta diversity of the communities of medium- to large bodied vertebrates inFrenchGuianan terra firme forests. Although the species studied are almost ubiquitous across the region, they exhibited habitat preferences through significant variation in abundance and in their association index with the different landscape types. As terra firme forests represent more than90{\%}of the Amazon basin, characterizing their heterogeneity – including faunal communities – is a major challenge in neotropical forest ecology.},
-author = {Richard-Hansen, C{\'{e}}cile and Jaouen, Ga{\"{e}}lle and Denis, Thomas and Brunaux, Olivier and Marcon, Eric and Guitet, St{\'{e}}phane},
-doi = {10.1017/S0266467415000255},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Richard-Hansen et al. - 2015 - Landscape patterns influence communities of medium- to large-bodied vertebrate in undisturbed terra firme.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {5},
-pages = {423--436},
-title = {{Landscape patterns influence communities of medium- to large-bodied vertebrate in undisturbed terra firme forests of French Guiana}},
-url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online{\&}aid=9884866{\&}fileId=S0266467415000255},
-volume = {31},
-year = {2015}
-}
-@article{Ricotta2012a,
-abstract = {Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species. {\textcopyright} 2012 Springer-Verlag.},
-annote = {Cited By (since 1996):4
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: OECOB
-PubMed ID: 22526936
-Language of Original Document: English
-Correspondence Address: Marignani, M.; Department of Life and Environmental Sciences, University of Cagliari, Viale S.Ignazio da Laconi 13, 09123 Cagliari, Italy; email: marignani@unica.it},
-author = {Ricotta, Carlo and Bacaro, Giovanni and Marignani, Michela and Godefroid, Sandrine and Mazzoleni, Stefano},
-doi = {10.1007/s00442-012-2318-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2012 - Computing diversity from dated phylogenies and taxonomic hierarchies Does it make a difference to the conclusion.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {501--506},
-title = {{Computing diversity from dated phylogenies and taxonomic hierarchies: Does it make a difference to the conclusions?}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84866331426{\&}partnerID=40{\&}md5=1be451df5db55f79928d409702192674},
-volume = {170},
-year = {2012}
-}
-@book{Bivand2008,
-abstract = {Instructional Book for using R for programming},
-author = {Bivand, Roger and Pebesma, Edzer J. and G{\'{o}}mez-Rubio, V.},
-booktitle = {Applied Spatial Data Analysis with R},
-doi = {10.1007/978-0-387-78171-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bivand, Pebesma, G{\'{o}}mez-Rubio - 2008 - Applied Spatial Data Analysis with R.pdf:pdf},
-isbn = {978-0-387-78170-9},
-title = {{Applied Spatial Data Analysis with R}},
-year = {2008}
-}
-@article{Adelman1969,
-abstract = {The H concentration measure (so designated because it was independently devised by 0. C. Herfindahl and A. 0. Hirschmann) is defined as the sum of squared percentages of market. (Thus with three firms of 0.5, 0.3 and 0.2, H would be 0.25 + 0.09 + 0.04 = 0.38.) It has not had a very wide use. In this note we (1) derive it from some general premises, and (2) show how it can be interpreted as a "numbers-equivalent" in any given market. (3) An important virtue both for com- puting and for using it is the quick convergence to a limit. Explaining its virtues will also show (4) its principal weakness.},
-author = {Adelman, M. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Adelman - 1969 - Comment on the H Concentration Measure as a Numbers-Equivalent.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {1},
-pages = {99--101},
-title = {{Comment on the "H" Concentration Measure as a Numbers-Equivalent}},
-url = {http://ideas.repec.org/a/tpr/restat/v51y1969i1p99-101.html},
-volume = {51},
-year = {1969}
-}
-@article{Bray1957,
-author = {Bray, J. Roger and Curtis, J. T.},
-doi = {10.2307/1942268},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bray, Curtis - 1957 - An Ordination of the Upland Forest Communities of Southern Wisconsin.pdf:pdf},
-journal = {Ecological Monographs},
-number = {4},
-pages = {325--349},
-title = {{An Ordination of the Upland Forest Communities of Southern Wisconsin}},
-url = {http://www.esajournals.org/action/showCitFormats?doi=10.2307/1942268},
-volume = {27},
-year = {1957}
-}
-@article{Weitzman1993,
-abstract = {This paper attempts to demonstrate how "diversity theory" can be applied to the analysis of real-world conservation policies. The specific example chosen to serve as a paradigm concerns preservation priorities among the fifteen species of cranes living wild throughout the world. The example is sufficiently actual to show how diversity theory can be used operationally to frame certain critical conservation questions and to guide us toward answers by providing informative quantitative indicators of what to protect. At the same time the cranes example is rich enough that it illustrates nicely some broad general principles about the economics of diversity preservation.},
-author = {Weitzman, Martin L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weitzman - 1993 - What to Preserve An Application of Diversity Theory to Crane Conservation.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {1},
-pages = {157--183},
-title = {{What to Preserve? An Application of Diversity Theory to Crane Conservation}},
-url = {http://www.jstor.org/stable/2118499},
-volume = {108},
-year = {1993}
-}
-@article{Stuart-Smith2013,
-abstract = {Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.},
-author = {Stuart-Smith, Rick D. and Bates, Amanda E. and Lefcheck, Jonathan S. and Duffy, J. Emmett and Baker, Susan C. and Thomson, Russell J. and Stuart-Smith, Jemina F. and Hill, Nicole A. and Kininmonth, Stuart J. and Airoldi, Laura and Becerro, Mikel A. and Campbell, Stuart J. and Dawson, Terence P. and Navarrete, Sergio A. and Soler, German A. and Strain, Elisabeth M. A. and Willis, Trevor J. and Edgar, Graham J.},
-doi = {10.1038/nature12529},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stuart-Smith et al. - 2013 - Integrating abundance and functional traits reveals new global hotspots of fish diversity.pdf:pdf},
-journal = {Nature},
-number = {7468},
-pages = {539--42},
-title = {{Integrating abundance and functional traits reveals new global hotspots of fish diversity.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/24067714},
-volume = {501},
-year = {2013}
-}
-@article{Mornet2013,
-abstract = {We propose a two-parameter subgroup decomposition method for the $\alpha$-Gini measures. • $\alpha$ denotes the inequality aversion and $\beta$ the sensitivity to non-overlappings. • The $\alpha$-Gini measures satisfy the usual principle of transfers according to $\alpha$. • A new between-group indicator is introduced: the economic $\beta$-directional distance. • The impact of group-progressive (resp. group-regressive) transfers is also analyzed.},
-author = {Mornet, Pauline and Zoli, Claudio and Mussard, St{\'{e}}phane and Sadefo-Kamdem, Jules and Seyte, Fran{\c{c}}oise and Terraza, Michel},
-doi = {10.1016/j.econmod.2013.06.016},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mornet et al. - 2013 - The ($\alpha$, $\beta$)-multi-level $\alpha$-Gini decomposition with an illustration to income inequality in France in 2005.pdf:pdf},
-journal = {Economic Modelling},
-pages = {944--963},
-title = {{The ($\alpha$, $\beta$)-multi-level $\alpha$-Gini decomposition with an illustration to income inequality in France in 2005}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0264999313002332},
-volume = {35},
-year = {2013}
-}
-@article{Wang2015,
-abstract = {Although trait information has been widely used to explore underlying mechanisms of forest community structure, most studies have focused on local patterns of phylogenetic or functional alpha diversity. Investigations of functional beta diversity, on the other hand, have not been conducted at local scales in a spatially explicit way. In this study, we provide a powerful methodology based on recent advances in spatial point pattern analysis using fully mapped data of large and small trees in two large temperate forest plots. This approach allowed us to assess the relative importance of different ecological processes and mechanisms for explaining patterns of local phylogenetic and functional beta diversity. For both forests and size classes, we found a clear hierarchy of scales: habitat filtering accounted for patterns of phylogenetic and functional beta diversity at larger distances (150–250 m), dispersal limitation accounted for the observed decline in beta diversity at distances below 150 m, and species interactions explained small departures from functional and phylogenetic beta diversity at the immediate plant-neighborhood scale (below 20 m). Thus, both habitat filtering and dispersal limitation influenced the observed patterns in phylogenetic and functional beta diversity at local scales. This result contrasts with a previous study from the same forests, where dispersal limitation alone approximated the observed species beta diversity for distances up to 250 m. In addition, species interactions were relatively unimportant for predicting phylogenetic and functional beta diversity. Our analysis suggests that phylogenetic and functional beta diversity can provide insights into the mechanisms of local community assembly that are missed by studies focusing exclusively on species beta diversity.},
-author = {Wang, Xugao and Wiegand, Thorsten and Swenson, Nathan G. and Wolf, Amy T. and Howe, Robert W. and Hao, Zhanqing and Lin, Fei and Ye, Ji and Yuan, Zuoqiang},
-doi = {10.1890/14-0392.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wang et al. - 2015 - Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1062--1073},
-title = {{Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/14-0392.1/abstract},
-volume = {96},
-year = {2015}
-}
-@article{Liebhold2002,
-abstract = {In many areas of ecology there is an increasing emphasis on spatial relationships. Often ecologists are interested in new ways of analyzing data with the objective of quantifying spatial patterns, and in designing surveys and experiments in light of the recognition that there may be underlying spatial pattern in biotic responses. In doing so, ecologists have adopted a number of widely different techniques and approaches derived from different schools of thought, and from other scientific disciplines. While the adaptation of a diverse array of statistical approaches and methodologies for the analysis of spatial data has yielded considerable insight into various ecological problems, this diversity of approaches has sometimes impeded communication and retarded more rapid progress in this emergent area. Many of these different statistical methods provide similar information about spatial characteristics, but the differences among these methods make it difficult to compare the results of studies that employ contrasting approaches. The papers in this mini-series explore possible areas of agreement and synthesis between a diversity of approaches to spatial analysis in ecology.},
-author = {Liebhold, A. M. and Gurevitch, J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liebhold, Gurevitch - 2002 - Integrating the Statistical Analysis of Spatial Data in Ecology.pdf:pdf},
-isbn = {09067590},
-journal = {Ecography},
-number = {5},
-pages = {553--557},
-title = {{Integrating the Statistical Analysis of Spatial Data in Ecology}},
-url = {http://www.jstor.org/stable/3683660},
-volume = {25},
-year = {2002}
-}
-@article{Chave2006,
-author = {Chave, J{\'{e}}r{\^{o}}me and Alonso, David and Etienne, Rampal S.},
-doi = {10.1038/nature04826},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Alonso, Etienne - 2006 - Theoretical biology - Comparing models of species abundance.pdf:pdf},
-journal = {Nature},
-number = {7089},
-pages = {E1--E1},
-title = {{Theoretical biology - Comparing models of species abundance}},
-volume = {441},
-year = {2006}
-}
-@article{Zhang2014c,
-abstract = {Diversity partitioning is becoming widely used to decompose the total number of species recorded in an area or region {\{}Mathematical expression{\}} into the average number of species within samples {\{}Mathematical expression{\}} and the average difference in species composition {\{}Mathematical expression{\}} among samples. Single-value metrics of {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} diversity are popular because they may be applied at multiple scales and because of their ease in computation and interpretation. Studies thus far, however, have emphasized observed diversity components or comparisons to randomized, null distributions. In addition, prediction of {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} components using environmental or spatial variables has been limited to more extensive data sets because multiple samples are required to estimate single {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} components. Lastly, observed diversity components do not incorporate variation in detection probabilities among species or samples. In this study, we used hierarchical Bayesian models of species abundances to provide predictions of {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} components in species richness and composition using environmental and spatial variables. We illustrate our approach using butterfly data collected from 26 grassland remnants to predict spatially nested patterns of {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} based on the predicted counts of butterflies. Diversity partitioning using a Bayesian hierarchical model incorporated variation in detection probabilities by butterfly species and habitat patches, and provided prediction intervals for {\{}Mathematical expression{\}} and {\{}Mathematical expression{\}} components using environmental and spatial variables. {\textcopyright} 2013 Springer Science+Business Media New York.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Zhang, Jing and Crist, Thomas O. and Hou, Peijie},
-doi = {10.1007/s10651-013-0271-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Crist, Hou - 2014 - Partitioning of $\alpha$ and $\beta$ diversity using hierarchical Bayesian modeling of species distribution and abundance.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {4},
-pages = {611--625},
-title = {{Partitioning of $\alpha$ and $\beta$ diversity using hierarchical Bayesian modeling of species distribution and abundance}},
-url = {http://link.springer.com/10.1007/s10651-013-0271-2},
-volume = {21},
-year = {2014}
-}
-@article{Mosblech2012,
-abstract = {The last glacial period was marked by multiple, abrupt reorganizations of ocean and atmosphere circulation. On thousand-year timescales, slowing of the Atlantic meridional overturning circulation was associated with cooling in the high northern latitudes, whereas strengthened circulation was linked to northern warming. In the tropics, these millennial-scale events were primarily reflected in altered patterns of precipitation. These hydrologic fluctuations induced ecological changes in the Atlantic seaboard and the high Andes, but less is known about the Amazon Basin. Here we reconstruct precipitation over Amazonian Ecuador over the past 94,000 years using a $\delta$18O record from speleothems collected in Santiago Cave in western Amazonia. We interpret the variability of the $\delta$18O record as changes in the source and amount of precipitation. With the exception of the period between 40,000 and 17,000 years ago, abrupt, high-frequency changes coincide with shifts in North Atlantic circulation, indicating a high-latitude influence on Amazonian precipitation over millennial timescales. On longer timescales, the record shows a relationship to precessional changes in the Earth's orbit. In light of the lack of extreme aridity in our records, we conclude that ecosystems in western Amazonia have not experienced prolonged drying over the past 94,000 years.},
-author = {Mosblech, Nicole A S and Bush, Mark B. and Gosling, William D. and Hodell, David and Thomas, Louise and {Van Calsteren}, Peter and Correa-Metrio, Alexander and Valencia, Bryan G. and Curtis, Jason and {Van Woesik}, Robert},
-doi = {10.1038/ngeo1588},
-isbn = {4019393974},
-issn = {17520894},
-journal = {Nature Geoscience},
-number = {11},
-pages = {817--820},
-title = {{North Atlantic forcing of Amazonian precipitation during the last ice age}},
-volume = {5},
-year = {2012}
-}
-@article{Drakare2006,
-abstract = {Species–area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.},
-author = {Drakare, Stina and Lennon, Jack J and Hillebrand, Helmut},
-doi = {10.1111/j.1461-0248.2005.00848.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Drakare, Lennon, Hillebrand - 2006 - The imprint of the geographical, evolutionary and ecological context on species–area relationships.pdf:pdf},
-journal = {Ecology Letters},
-number = {2},
-pages = {215--227},
-title = {{The imprint of the geographical, evolutionary and ecological context on species–area relationships}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2005.00848.x},
-volume = {9},
-year = {2006}
-}
-@article{Carmona2016,
-abstract = {Owing to the conceptual complexity of functional diversity (FD), a multitude of different methods are available for measuring it, with most being operational at only a small range of spatial scales. This causes uncertainty in ecological interpretations and limits the potential to generalize findings across studies or compare patterns across scales. We solve this problem by providing a unified framework expanding on and integrating existing approaches. The framework, based on trait probability density (TPD), is the first to fully implement the Hutchinsonian concept of the niche as a probabilistic hypervolume in estimating FD. This novel approach could revolutionize FD-based research by allowing quantification of the various FD components from organismal to macroecological scales, and allowing seamless transitions between scales. Functional trait diversity, in other words the variation of traits between organisms, can be used to address a great number of pressing ecological questions. Consequently, trait-based approaches are increasingly being used by ecologists.However, functional diversity comprises several components that can be evaluated at different spatial scales. Because of this conceptual complexity, there is an overabundance of disparate approaches for estimating it, which leads to confusion among users and hampers the comparability of different studies.A single mathematical framework encompassing different approaches while providing a seamless continuity between spatial scales is needed.Reconciling the approaches based on the concept of the niche as a hypervolume and those that consider traits in probabilistic terms is the first step towards the foundation of a unified framework.},
-author = {Carmona, Carlos P. and de Bello, Francesco and Mason, Norman W. H. and Lep{\v{s}}, Jan},
-doi = {10.1016/j.tree.2016.02.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carmona et al. - 2016 - Traits Without Borders Integrating Functional Diversity Across Scales.pdf:pdf},
-journal = {Trends in Ecology and Evolution},
-number = {5},
-pages = {382--394},
-title = {{Traits Without Borders: Integrating Functional Diversity Across Scales}},
-url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(16)00045-8},
-volume = {31},
-year = {2016}
-}
-@article{Mason2005,
-abstract = {Functional diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity - richness, evenness and divergence. These concepts are applied to functional characters to give three components of functional diversity - functional richness, functional evenness and functional divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem-function relationships.},
-author = {Mason, Norman W. H. and Mouillot, David and Lee, William G. and Wilson, J. Bastow},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mason et al. - 2005 - Functional richness, functional evenness and functional divergence the primary components of functional diversity.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {112--118},
-title = {{Functional richness, functional evenness and functional divergence: the primary components of functional diversity}},
-volume = {111},
-year = {2005}
-}
-@article{Hsieh2016,
-abstract = {Measures of phylogenetic diversity are basic tools in many studies of systematic biology. Faith's PD (sum of branch lengths of a phylogenetic tree connecting all focal species) is the most widely used phylogenetic measure. Like species richness, Faith's PD based on sampling data is highly dependent on sample size and sample completeness. The sample-size- and sample-coverage-based integration of rarefaction and extrapolation of Faith's PD was recently developed to make fair comparison across multiple assemblages. However, species abundances are not considered in Faith's PD. Based on the framework of Hill numbers, Faith's PD was generalized to a class of phylogenetic diversity measures that incorporates species abundances. In this paper, we develop both theoretical formulae and analytic estimators for seamless rarefaction and extrapolation for this class of abundance-sensitive phylogenetic measures, which includes simple transformations of phylogenetic entropy and of quadratic entropy. This work generalizes the previous rarefaction/extrapolation model of Faith's PD to incorporate species abundance, and also extends the previous rarefaction/extrapolation model of Hill numbers to include phylogenetic differences among species. Thus a unified approach to assessing and comparing species/taxonomic diversity and phylogenetic diversity can be established. A bootstrap method is suggested for constructing confidence intervals around the phylogenetic diversity, facilitating the comparison of multiple assemblages. Our formulation and estimators can be extended to incidence data collected from multiple sampling units. We also illustrate the formulae and estimators using bacterial sequence data from the human distal esophagus and phyllostomid bat data from three habitats.},
-author = {Hsieh, T. C. and Chao, Anne},
-doi = {10.1093/sysbio/syw073},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hsieh, Chao - 2016 - Rarefaction and Extrapolation Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple A.pdf:pdf},
-journal = {Systematic Biology},
-number = {1},
-pages = {syw073},
-title = {{Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages}},
-url = {http://sysbio.oxfordjournals.org/lookup/doi/10.1093/sysbio/syw073},
-volume = {66},
-year = {2016}
-}
-@unpublished{Scholl2012,
-abstract = {We present a new statistical method that detects industrial clusters at a firm level. The proposed method does not divide space into subunits whereby it is not affected by the Modifiable Areal Unit Problem (MAUP). Our metric differs both in its calcula- tion and interpretation from existing distance-based metrics and shows four central properties that enable its meaningful usage for cluster analysis. The method fulfills all five criteria for a test of localization proposed by Duranton and Overman (2005).},
-author = {Scholl, Tobias and Brenner, Thomas},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scholl, Brenner - 2012 - Detecting Spatial Clustering Using a Firm-Level Cluster Index.pdf:pdf},
-institution = {Philipps-Universit{\"{a}}t Marburg},
-series = {Working Papers on Innovation and Space},
-title = {{Detecting Spatial Clustering Using a Firm-Level Cluster Index}},
-year = {2012}
-}
-@article{Buckland2017,
-abstract = {In 2002, nearly 200 nations signed up to the 2010 target of the Convention for Biological Diversity, ‘to significantly reduce the rate of biodiversity loss by 2010'. To assess whether the target was met, it became necessary to quantify temporal trends in measures of diversity. This resulted in a marked shift in focus for biodiversity measurement. We explore the developments in measuring biodiversity that was prompted by the 2010 target. We consider measures based on species proportions, and also explain why a geometric mean of relative abundance estimates was preferred to such measures for assessing progress towards the target. We look at the use of diversity profiles, and consider how species similarity can be incorporated into diversity measures. We also discuss measures of turnover that can be used to quantify shifts in community composition arising, for example, from climate change.},
-author = {Buckland, Stephen T. and Yuan, Y. and Marcon, Eric},
-doi = {10.1007/s10182-017-0308-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Buckland, Yuan, Marcon - 2017 - Measuring temporal trends in biodiversity.pdf:pdf},
-journal = {AStA Advances in Statistical Analysis},
-number = {4},
-pages = {461--474},
-title = {{Measuring temporal trends in biodiversity}},
-url = {http://link.springer.com/10.1007/s10182-017-0308-1},
-volume = {101},
-year = {2017}
-}
-@article{Kwoka1981,
-annote = {Concentration industrielle. Indice Cn = part des n plus grosses firmes dans le secteur.},
-author = {Kwoka, John E. Jr},
-doi = {10.2307/2098257},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kwoka - 1981 - Does the choice of concentration measure really matter.pdf:pdf},
-journal = {The Journal of Industrial Economics},
-number = {4},
-pages = {445--453},
-title = {{Does the choice of concentration measure really matter?}},
-url = {http://www.jstor.org/stable/2098257},
-volume = {29},
-year = {1981}
-}
-@misc{Hardy2010,
-author = {Hardy, Olivier J.},
-title = {{BiodivR 1.2. A program to compute statistically unbiased indices of species diversity within sample and species similarity between samples using rarefaction principles}},
-url = {http://ebe.ulb.ac.be/ebe/Software.html},
-year = {2010}
-}
-@article{Short2010,
-abstract = {The mechanisms driving the nucleation, spread, and dissipation of crime hotspots are poorly understood. As a consequence, the ability of law enforcement agencies to use mapped crime patterns to design crime prevention strategies is severely hampered. We also lack robust expectations about how different policing interventions should impact crime. Here we present a mathematical framework based on reaction-diffusion partial differential equations for studying the dynamics of crime hotspots. The system of equations is based on empirical evidence for how offenders move and mix with potential victims or targets. Analysis shows that crime hotspots form when the enhanced risk of repeat crimes diffuses locally, but not so far as to bind distant crime together. Crime hotspots may form as either supercritical or subcritical bifurcations, the latter the result of large spikes in crime that override linearly stable, uniform crime distributions. Our mathematical methods show that subcritical crime hotspots may be permanently eradicated with police suppression, whereas supercritical hotspots are displaced following a characteristic spatial pattern. Our results thus provide a mechanistic explanation for recent failures to observe crime displacement in experimental field tests of hotspot policing.},
-author = {Short, Martin B. and Brantingham, P. Jeffrey and Bertozzi, Andrea L. and Tita, George E.},
-doi = {10.1073/pnas.0910921107},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Short et al. - 2010 - Dissipation and displacement of hotspots in reaction-diffusion models of crime.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {9},
-pages = {3961--3965},
-title = {{Dissipation and displacement of hotspots in reaction-diffusion models of crime}},
-url = {http://www.pnas.org/content/107/9/3961.abstract},
-volume = {107},
-year = {2010}
-}
-@article{Whittaker1977,
-author = {Whittaker, R. H.},
-editor = {Hecht, M. K. and Steere, W. C. and Wallace, B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker - 1977 - Evolution of species diversity in land communities.pdf:pdf},
-journal = {Evolutionary Biology},
-pages = {1--67},
-title = {{Evolution of species diversity in land communities}},
-volume = {10},
-year = {1977}
-}
-@incollection{Speth1992,
-address = {Washington, D.C.},
-author = {Speth, James Gustave and Holdgate, Martin W. and Tolba, Mostafa K.},
-booktitle = {Global Biodiversity Strategy},
-editor = {Courrier, Kathleen},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Speth, Holdgate, Tolba - 1992 - Foreword.pdf:pdf},
-pages = {v--vi},
-publisher = {WRI, IUCN, UNEP},
-title = {{Foreword}},
-year = {1992}
-}
-@article{Fisher1943,
-abstract = {A theoretical distribution is developed which appears to be suitable for the frequencies with which different species occur in a random collection, in the common case in which many species are so rare that their chance of inclusion is small. The relationships of the new distribution with the negative binomial and the Poisson series are estab- lished. Numerical processes are exhibited for fitting the series to observations containing given numbers of species and individuals, and for estimating the para- meter ac representing the richness in species of the material sampled; secondly, for calculating the stan- dard error of a, and thirdly, for testing whether the series exhibits a significant deviation from the limiting form used. Special tables are presented for facilitating these calculations.},
-author = {Fisher, R. A. and Corbet, A. Steven and Williams, Carrington Bonsor},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fisher, Corbet, Williams - 1943 - The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Anim.pdf:pdf},
-journal = {Journal of Animal Ecology},
-pages = {42--58},
-title = {{The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population}},
-volume = {12},
-year = {1943}
-}
-@article{Bordenave1998,
-abstract = {Des m{\'{e}}thodes de mesure de biodiversit{\'{e}} de diff{\'{e}}rents habitats forestiers, mises au point en Guyane, sont expos{\'{e}}es dans cet article : elles permettent d'analyser comparativement la diversit{\'{e}} sp{\'{e}}cifique et {\'{e}}cologique de diff{\'{e}}rentes for{\^{e}}ts {\`{a}} l'aide de courbes aire-esp{\`{e}}ces et d'indices de diversit{\'{e}} {\'{e}}tablis pour chaque composante du peuplement de plantes vasculaires. En plus de la connaissance fondamentale de la structure et de la composition floristique, indispensables {\`{a}} la compr{\'{e}}hension du fonctionnement de l'{\'{e}}cosyst{\`{e}}me forestier, ces nouveaux outils trouvent des applications concr{\`{e}}tes pour orienter les actions de gestion et de conservation du patrimoine naturel des for{\^{e}}ts guyanaises.},
-author = {Bordenave, Bruno Georges and {De Granville}, Jean-Jacques},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bordenave, De Granville - 1998 - Les mesures de la biodiversit{\'{e}} un outil de conservation en for{\^{e}}t guyanaise.pdf:pdf},
-journal = {JATBA, Revue d'Ethnobiologie},
-number = {1-2},
-pages = {433--446},
-title = {{Les mesures de la biodiversit{\'{e}} : un outil de conservation en for{\^{e}}t guyanaise}},
-url = {http://www.persee.fr/doc/jatba{\_}0183-5173{\_}1998{\_}num{\_}40{\_}1{\_}3684},
-volume = {40},
-year = {1998}
-}
-@article{Winter2013,
-abstract = {To date, there is little evidence that phylogenetic diversity has contributed to nature conservation. Here, we discuss the scientific justification of using phylogenetic diversity in conservation and the reasons for its neglect. We show that, apart from valuing the rarity and richness aspect, commonly quoted justifications based on the usage of phylogenetic diversity as a proxy for functional diversity or evolutionary potential are still based on uncertainties. We discuss how a missing guideline through the variety of phylogenetic diversity metrics and their relevance for conservation might be responsible for the hesitation to include phylogenetic diversity in conservation practice. We outline research routes that can help to ease uncertainties and bridge gaps between research and conservation with respect to phylogenetic diversity.},
-author = {Winter, Marten and Devictor, Vincent and Schweiger, Oliver},
-doi = {10.1016/j.tree.2012.10.015},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Winter, Devictor, Schweiger - 2013 - Phylogenetic diversity and nature conservation where are we.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {4},
-pages = {199--204},
-title = {{Phylogenetic diversity and nature conservation: where are we?}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534712002881},
-volume = {28},
-year = {2013}
-}
-@article{Redding2008,
-abstract = {Evolutionary distinctiveness measures of how evolutionarily isolated a species is relative to other members of its clade. Recently, distinctiveness metrics that explicitly incorporate time have been proposed for conservation prioritization. However, we found that such measures differ qualitatively in how well they capture the total amount of evolution (termed phylogenetic diversity, or PD) represented by a set of species. We used simulation and simple graph theory to explore this relationship with reference to phylogenetic tree shape. Overall, the distinctiveness measures capture more PD on more unbalanced trees and on trees with many splits near the present. The rank order of performance was robust across tree shapes, with apportioning measures performing best and node-based measures performing worst. A sample of 50 ultrametric trees from the literature showed the same patterns. Taken together, this suggests that distinctiveness metrics may be a useful addition to other measures of value for conservation prioritization of species. The simplest measure, the age of a species, performed surprisingly well, suggesting that new measures that focus on tree shape near the tips may provide a transparent alternative to more complicated full-tree approaches. {\textcopyright} 2008 Elsevier Ltd. All rights reserved.},
-author = {Redding, David W. and Hartmann, Klaas and Mimoto, Aki and Bokal, Drago and DeVos, Matt and Mooers, Arne {\O}.},
-doi = {10.1016/j.jtbi.2007.12.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Redding et al. - 2008 - Evolutionarily distinctive species often capture more phylogenetic diversity than expected.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {4},
-pages = {606--615},
-title = {{Evolutionarily distinctive species often capture more phylogenetic diversity than expected}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519307006285},
-volume = {251},
-year = {2008}
-}
-@article{Vu2007,
-abstract = {Data on 'neural coding' have frequently been analyzed using information-theoretic measures. These formulations involve the fundamental and generally difficult statistical problem of estimating entropy. We review briefly several methods that have been advanced to estimate entropy and highlight a method, the coverage-adjusted entropy estimator (CAE), due to Chao and Shen that appeared recently in the environmental statistics literature. This method begins with the elementary Horvitz-Thompson estimator, developed for sampling from a finite population, and adjusts for the potential new species that have not yet been observed in the sample - these become the new patterns or 'words' in a spike train that have not yet been observed. The adjustment is due to I. J. Good, and is called the Good-Turing coverage estimate. We provide a new empirical regularization derivation of the coverage-adjusted probability estimator, which shrinks the maximum likelihood estimate. We prove that the CAE is consistent and first-order optimal, with rate O P (1/log n), in the class of distributions with finite entropy variance and that, within the class of distributions with finite qth moment of the log-likelihood, the Good-Turing coverage estimate and the total probability of unobserved words converge at rate O P (1/(log n) q). We then provide a simulation study of the estimator with standard distributions and examples from neuronal data, where observations are dependent. The results show that, with a minor modification, the CAE performs much better than the MLE and is better than the best upper bound estimator, due to Paninski, when the number of possible words m is unknown or infinite. Copyright {\textcopyright} 2007 John Wiley {\&} Sons, Ltd.},
-annote = {Cited By (since 1996): 10
-Export Date: 15 November 2012
-Source: Scopus},
-author = {Vu, Vincent Q. and Yu, Bin and Kass, Robert E.},
-doi = {10.1002/sim.2942},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vu, Yu, Kass - 2007 - Coverage-adjusted entropy estimation.pdf:pdf},
-journal = {Statistics in Medicine},
-number = {21},
-pages = {4039--4060},
-title = {{Coverage-adjusted entropy estimation}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34548391942{\&}partnerID=40{\&}md5=046bf2951c790a7541c691f647c337cf},
-volume = {26},
-year = {2007}
-}
-@book{BioSavanne-Guyane2015,
-author = {{Bio Savanne - Guyane}},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bio Savanne - Guyane - 2015 - Cultivons autrement exemples locaux de techniques agro-{\'{e}}cologiques.pdf:pdf},
-isbn = {978-2-9553997-0-5},
-publisher = {Bio Savane},
-title = {{Cultivons autrement : exemples locaux de techniques agro-{\'{e}}cologiques}},
-year = {2015}
-}
-@article{Emerson2008,
-abstract = {Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly. ?? 2008 Elsevier Ltd. All rights reserved.},
-author = {Emerson, Brent C. and Gillespie, Rosemary G.},
-doi = {10.1016/j.tree.2008.07.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Emerson, Gillespie - 2008 - Phylogenetic analysis of community assembly and structure over space and time.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {11},
-pages = {619--630},
-title = {{Phylogenetic analysis of community assembly and structure over space and time}},
-volume = {23},
-year = {2008}
-}
-@article{Bacaro2013,
-abstract = {One of the goals of research in forest ecology is the development of simple indices as "proxies" in order to assess biological complexity in forests (e.g., structural and compositional diversity in forest stands). Many indices have been proposed to quantify forest stand diversity, but a general agreement on their use is yet not reached. Information theory and indices based on it are well-developed tools in ecological research and can respond to these requirements. In this short note, the recent literature on forest structural assessment is briefly summarized; then, one of the main properties of Shannon's entropy, namely the "recursivity", is proposed as a useful way for combining forest stand structure and species diversity into a single index. {\textcopyright} 2013 Taylor {\&} Francis.},
-annote = {Export Date: 12 March 2014
-Source: Scopus
-Article in Press
-Language of Original Document: English
-Correspondence Address: Bacaro, G.; CNR-IRPI, Istituto di Ricerca per la Protezione Idrogeologica, Via Madonna Alta 126, 06128, Perugia,email: bacaro@unisi.it},
-author = {Bacaro, Giovanni and Ricotta, Carlo and Marignani, Michela and Torri, Dino and Chiarucci, Alessandro},
-doi = {10.1080/14728028.2013.844933},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro et al. - 2014 - Using Shannon's recursivity to summarize forest structural diversity.pdf:pdf},
-journal = {Forests Trees and Livelihoods},
-number = {3},
-pages = {211--216},
-title = {{Using Shannon's recursivity to summarize forest structural diversity}},
-url = {http://www.tandfonline.com/doi/pdf/10.1080/14728028.2013.844933},
-volume = {23},
-year = {2014}
-}
-@article{Chesson2000,
-abstract = {The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence, in which species diversity slowly decays over time, have focused almost exclusively on equalizing mechanisms. These models would be more robust if they also included stabilizing mechanisms, which arise in many and varied ways but need not be adequate for full stability of a system. Models of unstable coexistence invite a broader view of diversity maintenance incorporating species turnover.},
-author = {Chesson, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chesson - 2000 - Mechanisms of maintenance of species diversity.pdf:pdf},
-journal = {Annual review of Ecology and Systematics},
-pages = {343--366},
-title = {{Mechanisms of maintenance of species diversity}},
-url = {http://www.jstor.org/stable/221736},
-volume = {31},
-year = {2000}
-}
-@article{Villeger2008a,
-abstract = {Functional diversity is increasingly identified as an important driver of ecosystem functioning. Various indices have been proposed to measure the functional diversity of a community, but there is still no consensus on which are most suitable. Indeed, none of the existing indices meets all the criteria required for general use. The main criteria are that they must be designed to deal with several traits, take into account abundances, and measure all the facets of functional diversity. Here we propose three indices to quantify each facet of functional diversity for a community with species distributed in a multidimensional functional space: functional richness (volume of the functional space occupied by the community), functional evenness (regularity of the distribution of abundance in this volume), and functional divergence (divergence in the distribution of abundance in this volume). Functional richness is estimated using the existing convex hull volume index. The new functional evenness index is based on the minimum spanning tree which links all the species in the multidimensional functional space. Then this new index quantifies the regularity with which species abundances are distributed along the spanning tree. Functional divergence is measured using a novel index which quantifies how species diverge in their distances (weighted by their abundance) from the center of gravity in the functional space. We show that none of the indices meets all the criteria required for a functional diversity index, but instead we show that the set of three complementary indices meets these criteria. Through simulations of artificial data sets, we demonstrate that functional divergence and functional evenness are independent of species richness and that the three functional diversity indices are independent of each other. Overall, our study suggests that decomposition of functional diversity into its three primary components provides a meaningful framework for its quantification and for the classification of existing functional diversity indices. This decomposition has the potential to shed light on the role of biodiversity on ecosystem functioning and on the influence of biotic and abiotic filters on the structure of species communities. Finally, we propose a general framework for applying these three functional diversity indices.},
-author = {Vill{\'{e}}ger, S{\'{e}}bastien and Mason, Norman W. H. and Mouillot, David},
-doi = {10.1890/07-1206.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vill{\'{e}}ger, Mason, Mouillot - 2008 - New multidimensional functional diversity indices for a multifaceted framework in functional ecology.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2290--2301},
-title = {{New multidimensional functional diversity indices for a multifaceted framework in functional ecology}},
-url = {http://www.esajournals.org/doi/abs/10.1890/07-1206.1},
-volume = {89},
-year = {2008}
-}
-@article{Law2009,
-abstract = {1. This article reviews the application of some summary statistics from current theory of spatial point processes for extracting information from spatial patterns of plants. Theoretical measures and issues connected with their estimation are described. Results are illustrated in the context of specific ecological questions about spatial patterns of trees in two forests. 2. The pair correlation function, related to Ripley's K function, provides a formal measure of the density of neighbouring plants and makes precise the general notion of a 'plant's-eye' view of a community. The pair correlation function can also be used to describe spatial relationships of neighbouring plants with different qualitative properties, such as species identity and size class. 3. The mark correlation function can be used to describe the spatial relationships of quantitative measures (e.g. biomass). We discuss two types of correlation function for quantitative marks. Applying these functions to the distribution of biomass in a temperate forest, it is shown that the spatial pattern of biomass is uncoupled from the spatial pattern of plant locations. 4. The inhomogeneous pair correlation function enables first-order heterogeneity in the environment to be removed from second-order spatial statistics. We illustrate this for a tree species in a forest of high topographic heterogeneity and show that spatial aggregation remains after allowing for spatial variation in density. An alternative method, the master function, takes a weighted average of homogeneous pair correlation functions computed in subareas; when applied to the same data and compared with the former method, the spatial aggregations are smaller in size. 5. Synthesis. These spatial statistics, especially those derived from pair densities, will help ecologists to extract important ecological information from intricate spatially correlated plants in populations and communities.},
-annote = {ISI Document Delivery No.: 459AG
-Times Cited: 2
-Cited Reference Count: 59
-Law, Richard Illian, Janine Burslem, David F. R. P. Gratzer, Georg Gunatilleke, C. V. S. Gunatilleke, I. A. U. N.
-WILEY-BLACKWELL PUBLISHING, INC},
-author = {Law, Richard and Illian, Ja and Burslem, David F. R. P. and Gratzer, Georg and Gunatilleke, C. V. S. and Gunatilleke, I. A. U. N.},
-doi = {10.1111/j.1365-2745.2009.01510.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Law et al. - 2009 - Ecological information from spatial patterns of plants insights from point process theory.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {616--628},
-title = {{Ecological information from spatial patterns of plants: insights from point process theory}},
-volume = {97},
-year = {2009}
-}
-@article{Dong2015,
-abstract = {Patterns of b diversity are commonly used to infer underlying ecological processes. In this study, we examined the effect of spatial configuration of habitat capacity on different metrics of b diversity, i.e., b diversity measured as turnover and as variation. For b diversity as turnover, a monotonic species spatial turnover pattern is typically considered as a benchmark for species distributions driven only by dispersal process. Deviations from a monotonic curve are attributed to local environmental filtering (i.e., the same environmental factors affecting different species differently). However, we found non- monotonicity in species spatial turnover in models without environmental filtering effect. This non- monotonicity was caused by variation in a diversity, introduced by spatial configuration of habitat capacity. After applying a recent null-model approach—designed to tease out the effect of variation in a diversity—species spatial turnover remained non-monotonic. This non-monotonicity makes it problematic to use species spatial turnover to infer the underlying processes for species distribution, i.e., whether it is driven by environmental filtering or dispersal processes. Spatial configuration of habitat capacity also influences landscape connectivity. Small-habitat capacity sites may constrain movements of organisms (i.e., dispersal) between sites supporting high capacity habitats. We showed that in a landscape where small- habitat capacity sites were located in positions important for dispersal (e.g., in the center as opposed to on the edge of a landscape) has a higher spatial variation of species composition, hence, higher b diversity. Ecologists who use different measures of b diversity should be aware of these effects introduced by spatial configuration of habitat capacity.},
-author = {Dong, X. and Muneepeerakul, R. and Olden, J. D. and Lytle, D. A.},
-doi = {10.1890/ES14-00497.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dong et al. - 2015 - The effect of spatial configuration of habitat capacity on b diversity.pdf:pdf},
-journal = {Ecosphere},
-number = {11},
-pages = {Article 220},
-title = {{The effect of spatial configuration of habitat capacity on b diversity}},
-volume = {6},
-year = {2015}
-}
-@article{Shipley2016,
-abstract = {The promise of “trait-based” plant ecology is one of generalized prediction across organizational and spatial scales, independent of taxonomy. This promise is a major reason for the increased popularity of this approach. Here, we argue that some important foundational assumptions of trait-based ecology have not received sufficient empirical evaluation. We identify three such assumptions and, where possible, suggest methods of improvement: (i) traits are functional to the degree that they determine individual fitness, (ii) intraspecific variation in functional traits can be largely ignored, and (iii) functional traits show general predictive relationships to measurable environmental gradients .},
-author = {Shipley, Bill and {De Bello}, Francesco and Cornelissen, J. Hans C. and Lalibert{\'{e}}, Etienne and Laughlin, Daniel C. and Reich, Peter B.},
-doi = {10.1007/s00442-016-3549-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shipley et al. - 2016 - Reinforcing loose foundation stones in trait-based plant ecology.pdf:pdf},
-journal = {Oecologia},
-number = {4},
-pages = {923--931},
-title = {{Reinforcing loose foundation stones in trait-based plant ecology}},
-url = {https://link.springer.com/article/10.1007/s00442-016-3549-x},
-volume = {180},
-year = {2016}
-}
-@article{Besag1991,
-abstract = {Tests for clustering of rare diseases investigate whether an observed pattern of cases in one or more geographical regions could reasonably have arisen by chance alone, bearing in mind the variation in background population density. In contrast, tests for the detection of clusters are concerned with screening a large region for evidence of individual ‘hot spots' of disease but without any preconception about their likely locations; the results of such tests may form the basis for subsequent small area investigations, statistical or non-statistical, but will rarely be an end in themselves. The main intention of the paper is to describe and illustrate a new technique for the identification of small clusters of disease. A secondary purpose is to discuss some common pitfalls in the application of tests of clustering to epidemiological data.},
-author = {Besag, Julian E. and Newell, James},
-doi = {10.2307/2982708},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Besag, Newell - 1991 - The Detection of Clusters in Rare Diseases.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {1},
-pages = {143--155},
-title = {{The Detection of Clusters in Rare Diseases}},
-url = {http://www.jstor.org/stable/2982708},
-volume = {154},
-year = {1991}
-}
-@article{Kraft2010,
-abstract = {Despite a long history of the study of tropical forests, uncertainty about the importance of different ecological processes in shaping tropical tree species distributions persists. Trait- and phylogenetic-based tests of community assembly provide a powerful way to detect community assembly processes but have seldom been applied to the same community. Both methods are well suited to testing how the relative importance of different ecological processes changes with spatial scale. Here we apply both methods to the Yasun{\'{i}} Forest Dynamics Plot, a 25-ha Amazonian forest with {\textgreater}1100 tree species. We found evidence for habitat filtering from both trait and phylogenetic methods from small (25 m2) to intermediate (10 000 m2) spatial scales. Trait-based methods detected even spacing of strategies, a pattern consistent with niche partitioning or enemy-mediated density dependence, at smaller spatial scales (25–400 m2). Simulation modeling of community assembly processes suggests that low statistical power to detect even spacing of traits at larger spatial scales may contribute to the observed patterns. Trait and phylogenetic methods tended to identify the same areas of the forest as being subject to habitat filtering. Phylogenetic community tests, which are far less data-intensive than trait-based methods, captured much of the same filtering patterns detected by trait-based methods but often failed to detect even-spacing patterns apparent in trait data. Taken together, it appears that both habitat associations and niche differentiation shape species co-occurrence patterns in one of the most diverse forests in the world at a range of small and intermediate spatial scales.},
-author = {Kraft, Nathan J. B. and Ackerly, David D.},
-doi = {10.1890/09-1672.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kraft, Ackerly - 2010 - Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {401--422},
-title = {{Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-1672.1},
-volume = {80},
-year = {2010}
-}
-@article{Duranton2000,
-abstract = {Why are some cities specialised and others diversified? What are the advantages and disadvantages of urban specialisation and diversity? To what extent do the structure of cities and the activities of firms and people in them change over time? How does the sectoral composition of cities influence their evolution? To answer these and related questions, we first distil some key stylised facts from the empirical literature on cities and the composition of their activities. We then turn to a review of different theories looking at such issues, and study the extent to which these theories contribute to the understanding of the empirical regularities.},
-author = {Duranton, Gilles and Puga, Diego},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton, Puga - 2000 - Diversity and Specialisation in Cities Why, Where and When does it Matter.pdf:pdf},
-journal = {Urban Studies},
-number = {3},
-pages = {533--555},
-title = {{Diversity and Specialisation in Cities: Why, Where and When does it Matter?}},
-url = {http://journals.sagepub.com/doi/abs/10.1080/0042098002104},
-volume = {37},
-year = {2000}
-}
-@article{Moran1950,
-author = {Moran, P .A . P.},
-doi = {10.2307/2332142},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moran - 1950 - Notes on continuous stochastic phenomena.pdf:pdf},
-journal = {Biometrika},
-number = {1/2},
-pages = {17--23},
-title = {{Notes on continuous stochastic phenomena}},
-url = {http://www.jstor.org/stable/2332142},
-volume = {37},
-year = {1950}
-}
-@article{Keeley2005,
-abstract = {Question: Do rectangular sample plots record more plant species than square plots as suggested by both empirical and theoretical studies? Location: Grasslands, shrublands and forests in the Mediterranean-climate region of California, USA. Methods: We compared three 0.1-ha sampling designs that differed in the shape and dispersion of 1-m(2) and 100-m(2) nested subplots. We duplicated an earlier study that compared the Whittaker sample design, which had square clustered subplots, with the modified Whittaker design, which had dispersed rectangular subplots. To sort out effects of dispersion from shape we used a third design that overlaid square subplots on the modified Whittaker design. Also, using data from published studies we extracted species richness values for 400-m(2) subplots that were either square or 1:4 rectangles partially overlaid on each other from desert scrub in high and low rainfall years, chaparral, sage scrub, oak savanna and coniferous forests with and without fire. Results: We found that earlier empirical reports of more than 30{\%} greater richness with rectangles were due to the confusion of shape effects with spatial effects, coupled with the use of cumulative number of species as the metric for comparison. Average species richness was not significantly different between square and 1:4 rectangular sample plots at either I or 100-m2. Pairwise comparisons showed no significant difference between square and rectangular samples in all but one vegetation type, and that one exhibited significantly greater richness with squares. Our three intensive study sites appear to exhibit some level of self-similarity at the scale of 400 m(2), but, contrary to theoretical expectations, we could not detect plot shape effects on species richness at this scale. Conclusions: At the 0.1-ha scale or lower there is no evidence that plot shape has predictable effects on number of species recorded from sample plots. We hypothesize that for the mediterranean-climate vegetation types studied here, the primary reason that 1:4 rectangles do not sample greater species richness than squares is because species turnover varies along complex environmental gradients that are both parallel and perpendicular to the long axis of rectangular plots. Reports in the literature of much greater species richness recorded for highly elongated rectangular strips than for squares of the same area are not likely to be fair comparisons because of the dramatically different periphery/area ratio. which includes a much greater proportion of species that are using both above and below-ground niche space outside the sample area},
-author = {Keeley, Jon E and Fotheringham, C J},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Keeley, Fotheringham - 2005 - Plot Shape Effects on Plant Species Diversity Measurements.pdf:pdf},
-issn = {1100-9233},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {249--256},
-title = {{Plot Shape Effects on Plant Species Diversity Measurements}},
-volume = {16},
-year = {2005}
-}
-@article{Wai-ChungYeung2000,
-author = {{Wai-Chung Yeung}, Henry},
-doi = {10.1191/030913200671984115},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wai-Chung Yeung - 2000 - Organizing ‘the firm' in industrial geography I networks, institutions and regional development.pdf:pdf},
-journal = {Progress in Human Geography},
-number = {2},
-pages = {301--315},
-title = {{Organizing ‘the firm' in industrial geography I: networks, institutions and regional development}},
-url = {http://journals.sagepub.com/doi/abs/10.1191/030913200671984115},
-volume = {24},
-year = {2000}
-}
-@article{Ricotta2010a,
-author = {Ricotta, Carlo},
-doi = {doi:10.1890/09-0126.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2010 - On beta diversity decomposition Trouble shared is not trouble halved.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1981--1983},
-title = {{On beta diversity decomposition: Trouble shared is not trouble halved}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-0126.1},
-volume = {91},
-year = {2010}
-}
-@article{Schladitz2000,
-abstract = {Second order characteristics, in particular Ripley's K-function, are widely used for the statistical analysis of point patterns. We examine a third order analogue, namely the mean number T(r) of r-close triples of points per unit area. Equivalently this is the expected number of r-close point pairs in an r-neighbourhood of the typical point. Various estimators for this function are proposed and compared, and we give an explicit formula for the isotropic edge correction. The theoretical value of T seems to be unobtainable for most point process models apart from the homogeneous Poisson process. However, simulation studies show that the function T discriminates well between different types of point processes. In particular it detects a clear difference between the Poisson process and the Baddeley-Silverman cell process whereas the K-functions for these processes coincide.},
-annote = {Article
-English
-SCAND J STATIST
-377VC},
-author = {Schladitz, K. and Baddeley, Adrian J.},
-doi = {10.1111/1467-9469.00214},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schladitz, Baddeley - 2000 - A third order point process characteristic(2).pdf:pdf},
-journal = {Scandinavian Journal of Statistics},
-number = {4},
-pages = {657--671},
-title = {{A third order point process characteristic}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9469.00214/abstract},
-volume = {27},
-year = {2000}
-}
-@article{Ricotta2014,
-abstract = {Functional evenness is increasingly considered an important facet of functional diversity that sheds light on the complex relationships between community assembly and ecosystem functioning. Nonetheless, in spite of its relevant role for ecosystem functioning, only a few measures of functional evenness have been proposed. In this paper we introduce a new measure of functional evenness that reflects the regularity in the distribution of species abundances, together with the evenness in their pairwise functional dissimilarities. To show how the proposed measure works, we focus on changes in functional evenness calculated from Grime's classification of plant strategies as competitors (C), stress-tolerators (S) and ruderals (R) along a post-fire successional gradient in temperate chestnut forests of southern Switzerland.},
-author = {Ricotta, Carlo and Bacaro, Giovanni and Moretti, Marco},
-doi = {10.1371/journal.pone.0104060},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Bacaro, Moretti - 2014 - A new measure of functional evenness and some of its properties.pdf:pdf},
-journal = {PloS one},
-number = {8},
-pages = {e104060},
-title = {{A new measure of functional evenness and some of its properties.}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104060},
-volume = {9},
-year = {2014}
-}
-@incollection{Chave2007,
-address = {Santa Fe},
-author = {Chave, J{\'{e}}r{\^{o}}me and Chust, Guillem and Th{\'{e}}baud, Christophe},
-booktitle = {Scaling biodiversity},
-editor = {Storch, D. and Marquet, P. and Brown, J.H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Chust, Th{\'{e}}baud - 2007 - The importance of phylogenetic structure in biodiversity studies.pdf:pdf},
-pages = {150--167},
-publisher = {Institute Editions},
-title = {{The importance of phylogenetic structure in biodiversity studies}},
-url = {http://www.edb.ups-tlse.fr/equipe1/chave/chave-scaling07.pdf},
-year = {2007}
-}
-@article{Jensen1906,
-author = {Jensen, J. L. W. V.},
-doi = {10.1007/bf02418571},
-journal = {Acta Mathematica},
-language = {French},
-number = {1},
-pages = {175--193},
-title = {{Sur les fonctions convexes et les in{\'{e}}galit{\'{e}}s entre les valeurs moyennes}},
-url = {http://dx.doi.org/10.1007/BF02418571},
-volume = {30},
-year = {1906}
-}
-@article{Pelissier2003,
-abstract = {Both the ordination of taxonomic tables and the measurements of species diversity aim to capture the prominent features of the species composition of a community. However, interrelations between ordination techniques and diversity measurements are seldom explicated and are mainly ignored by many field ecologists. This paper starts from the notion of the species occurrence table, which provides a unifying formulation for different kinds of taxonomic data, Here it is demonstrated that alternative species weightings can be used to equate the total inertia of a centered-by-species occurrence table with common diversity indices, such as species richness, Simpson diversity, or Shannon information. Such an equation defines two main ordination strategies related to two different but consistent measures of species diversity. The first places emphasis on scarce species and is based on Correspondence Analysis and species richness (CA-richness strategy). The second, in which abundant species are prominent, relies on Non-Symmetric Correspondence Analysis and Simpson diversity (NSCA-Simpson strategy). Both strategies are suitable for measuring alpha and beta diversity by analyzing the centered-by-species, occurrence table with respect to external environmental or instrumental variables. In this paper, these two strategies are applied to ecological data obtained in a Neotropical rainforest plot. The results are then discussed with respect to the intrinsic characteristics of the community under analysis, and also to the broad classes of floro-faunistic data used in ecology (i.e., data gathered from museum or herbarium collections, exhaustive inventories in a reference plot, or enumeration through species-by-releves tables), The approach encompasses several well-known techniques such as Correspondence Analysis, Non-Symmetric Correspondence Analysis, Canonical Correspondence Analysis. and Redundancy Analysis, and provides greater insight into interrelations between ordination methods and diversity studies.},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l and Couteron, Pierre and Dray, St{\'{e}}phane and Sabatier, Daniel},
-doi = {10.1890/0012-9658(2003)084[0242:CBOTAD]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/P{\'{e}}lissier et al. - 2003 - Consistency between ordination techniques and diversity measurements Two strategies for species occurrence dat.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {242--251},
-title = {{Consistency between ordination techniques and diversity measurements: Two strategies for species occurrence data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282003{\%}29084[0242:CBOTAD]2.0.CO;2/full},
-volume = {84},
-year = {2003}
-}
-@article{Wright2006,
-abstract = {Background and Aims When ecologically important plant traits are correlated they may be said to constitute an ecological 'strategy' dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests.},
-author = {Wright, Ian J. and Ackerly, David D. and Bongers, Frans and Harms, Kyle E. and Ibarra-Manriquez, Guillermo and Martinez-Ramos, Miguel and Mazer, Susan J. and Muller-Landau, Helene C. and Paz, Horacio and Pitman, Nigel C. A. and Poorter, Lourens and Silman, Miles R. and Vriesendorp, Corine F. and Webb, Campbell O. and Westoby, Mark and Wright, S. Joseph},
-doi = {10.1093/aob/mcl066},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2006 - Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests.pdf:pdf},
-journal = {Annals of Botany},
-title = {{Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests}},
-year = {2006}
-}
-@article{Laughlin2014,
-abstract = {1. Plants are multifaceted organisms that have evolved numerous solutions to the problem of establishing, growing and reproducing with limited resources. The intrinsic dimensionality of plant traits is the minimum number of independent axes of variation that adequately describes the functional variation among plants and is therefore a fundamental quantity in comparative plant ecology. Given the large number of functional traits that aremeasured on plants, the dimensionality of plant form and function is potentially vast. 2. Avariety of linear and nonlinearmethodswere used to estimate the intrinsic dimensionality of three large trait data sets. The results of these analyses indicate that while the dimensionality of plant traits is generally larger than we have admitted in the past, it does not exceed six in themost comprehensive data set. 3. The dimensionality of plant form and function is a blessing, not a curse. The higher the intrinsic dimension of traits in an analysis, the more easily our models will be able to accurately discriminate species in trait space and therefore be able to predict species distributions and abundances. Recent analyses indicate that the ability to predict community composition increases rapidly with additional traits, but reaches a plateau after four to eight traits. 4. Synthesis. There appears to be a tractable upper limit to the dimensionality of plant traits. To optimize research efficiency for advancing our understanding of trait-based community assembly, ecologists should minimize the number of traits while maximizing the number of dimensions, because including multiple correlated traits does not yield dividends and including more than eight traits leads to diminishing returns. It is recommended to measure traits from multiple organs when- ever possible, especially leaf, stem, root and flowering traits, given their consistent performance in explaining},
-author = {Laughlin, Daniel C.},
-doi = {10.1111/1365-2745.12187},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Laughlin - 2014 - The intrinsic dimensionality of plant traits and its relevance to community assembly.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {186--193},
-title = {{The intrinsic dimensionality of plant traits and its relevance to community assembly}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12187/abstract},
-volume = {102},
-year = {2014}
-}
-@article{Ugland2003,
-abstract = {1One of the general characteristics of ecological communities is that the number of species accumulates with increasing area sampled. However, it is important to distinguish between the species–area relationship and species accumulation curves. The species–area relationship is concerned with the number of species in areas of different size irrespective of the identity of the species within the areas, whereas the species accumulation curve is concerned with accumulation rates of new species over the sampled area and depends on species identity. 2We derive an exact analytical expression for the expectance and variance of the species–accumulation curve in all random subsets of samples from a given area. The analytical species accumulation curve may be approximated by a semilog curve. Both the exact accumulation curve and its semilog approximation are independent of the underlying species abundance distributions, but are influenced strongly by the distribution of species among the samples and the spatial relationship of the samples that are randomized. 3To estimate species richness in larger areas than that sampled we take account of the spatial relationship between samples by dividing the sampled area into subareas. First a species–accumulation curve is obtained for randomized samples of all the single subareas. Then the species–accumulation curve for all combinations of two subareas is calculated and the procedure is repeated for all subareas. From these curves a new total species (T–S) curve is obtained from the terminal point of the subarea plots. The T–S curve can then be extrapolated to estimate the probable total number of species in the area studied. 4Data from the Norwegian continental shelf show that extrapolation of the traditional species–accumulation curve gave a large underestimate of total species richness for the whole shelf compared with that predicted by the T–S curve. Application of non-parametric methods also gave large underestimates compared with actual data obtained from more extensive sampling than the data analysed here. Although marine soft sediments sampled in Hong Kong were not as variable as those from the Norwegian shelf, nevertheless here the new method also gave higher estimates of total richness than the traditional species–accumulation approaches. 5Our data show that both the species–accumulation curve and the accompanying T–S curve apply to large heterogeneous areas varying in depth and sediment properties as well as a relatively small homogeneous area with small variation in depth and sediment properties.},
-author = {Ugland, Karl I. and Gray, John S. and Ellingsen, Kari E.},
-doi = {10.1046/j.1365-2656.2003.00748.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ugland, Gray, Ellingsen - 2003 - The species-accumulation curve and estimation of species richness.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {5},
-pages = {888 -- 897},
-title = {{The species-accumulation curve and estimation of species richness}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2003.00748.x/abstract},
-volume = {72},
-year = {2003}
-}
-@article{Ellerman2013,
-author = {Ellerman, David},
-doi = {10.1142/S1793351X13400059},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ellerman - 2013 - An Introduction To Logical Entropy and Its Relation To Shannon Entropy.pdf:pdf},
-journal = {International Journal of Semantic Computing},
-number = {02},
-pages = {121--145},
-title = {{An Introduction To Logical Entropy and Its Relation To Shannon Entropy}},
-url = {http://www.worldscientific.com/doi/abs/10.1142/S1793351X13400059},
-volume = {7},
-year = {2013}
-}
-@article{Su2016,
-abstract = {Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf–Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the “dominance” of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity.},
-author = {Su, Qiang},
-doi = {10.1016/j.jtbi.2015.12.010},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Su - 2016 - Analyzing fractal property of species abundance distribution and diversity indexes.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-pages = {107--112},
-title = {{Analyzing fractal property of species abundance distribution and diversity indexes}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0022519315006013},
-volume = {392},
-year = {2016}
-}
-@article{Veech2002,
-abstract = {Ecologists have traditionally viewed the total species diversity within a set of communities as the product of the average diversity within a community (alpha) and the diversity among the communities (beta). This multiplicative concept of species diversity contrasts with the lesser known idea that alpha- and beta-diversities sum to give the total diversity. This additive partitioning of species diversity is nearly as old as the multiplicative concept, yet ecologists are just now beginning to use additive partitioning to examine patterns of species diversity. In this review we discuss why additive partitioning remained "hidden" until just a few years ago. The rediscovery of additive partitioning has expanded the way in which ecologists define and measure beta-diversity. Beta diversity is no longer relegated to describing change only along all environmental gradient. Through additive partitioning, beta-diversity is explicitly an average amount of diversity just as is a-diversity. We believe that the additive partitioning of diversity into alpha and beta components will continue to become more widely used because it allows for a direct comparison of alpha- and beta-diversities. It also has particular relevance for testing ecological theory concerned with the determinants of species diversity at multiple spatial scales and potential applications ill conservation biology.},
-author = {Veech, Joseph A. and Summerville, Keith S. and Crist, Thomas O. and Gering, Jon C.},
-doi = {10.1034/j.1600-0706.2002.990101.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veech et al. - 2002 - The additive partitioning of species diversity recent revival of an old idea.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {3--9},
-title = {{The additive partitioning of species diversity: recent revival of an old idea}},
-url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2002.990101.x/abstract},
-volume = {99},
-year = {2002}
-}
-@article{Palareti2016,
-abstract = {Beta diversity is an important metric in ecology quantifying differentiation or disparity in composition among communities, ecosystems, or phenotypes. To compare systems with different sizes (N, number of units within a system), beta diversity is often converted to related indices such as turnover or local/regional differentiation. Here we use simulations to demonstrate that these naive measures of dissimilarity depend on sample size and design. We show that when N is the number of sampled units (e.g., quadrats) rather than the “true” number of communities in the system (if such exists), these differentiation measures are biased estimators. We propose using average pairwise dissimilarity as an intuitive solution. That is, instead of attempting to estimate an N-community measure, we advocate estimating the expected dissimilarity between any random pairs of communities (or sampling units)—especially when the “true” N is unknown or undefined. Fortunately, measures of pairwise dissimilarity or overlap have been used in ecology for decades, and their properties are well known. Using the same simulations, we show that average pairwise metrics give consistent and unbiased estimates regardless of the number of survey units sampled. We advocate pairwise dissimilarity as a general standardization to ensure commensurability of different study systems.},
-author = {Marion, Zachary H. and Fordyce, James A. and Fitzpatrick, Benjamin M.},
-doi = {10.1111/ijlh.12426},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marion, Fordyce, Fitzpatrick - 2017 - Pairwise beta diversity resolves an underappreciated source of confusion in calculating species tu.pdf:pdf},
-journal = {Ecology},
-title = {{Pairwise beta diversity resolves an underappreciated source of confusion in calculating species turnover}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/ecy.1753/full},
-volume = {in press},
-year = {2017}
-}
-@article{Cartozo2008,
-abstract = {We analyze several florae (collections of plant species populating specific areas) in different geographic and climatic regions. For every list of species we produce a taxonomic classification tree and we consider its statistical properties. We find that regardless of the geographical location, the climate and the environment all species collections have universal statistical properties that we show to be also robust in time. We then compare observed data sets with simulated communities obtained by randomly sampling a large pool of species from all over the world. We find differences in the behavior of the statistical properties of the corresponding taxonomic trees. Our results suggest that it is possible to distinguish quantitatively real species assemblages from random collections and thus demonstrate the existence of correlations between species. {\textcopyright} 2008 IOP Publishing Ltd.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-Art. No.: 224012
-Language of Original Document: English
-Correspondence Address: Cartozo, C. C.; Laboratoire de Biophysique Statistique, ITP-FSB, Ecole Polytechnique F{\'{e}}d{\'{e}}rale de Lausanne, CH-1015 Lausanne, Switzerland; email: cecile.carettacartozo@epfl.ch},
-author = {Cartozo, Cecile Caretta and Garlaschelli, Diego and Ricotta, Carlo and Barth{\'{e}}lemy, Marc and Caldarelli, Guido},
-doi = {10.1088/1751-8113/41/22/224012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cartozo et al. - 2008 - Quantifying the taxonomic diversity in real species communities.pdf:pdf},
-journal = {Journal of Physics A: Mathematical and Theoretical},
-pages = {224012},
-title = {{Quantifying the taxonomic diversity in real species communities}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-44449174070{\&}partnerID=40{\&}md5=b20368da61e17dbff6753c95857bef70},
-volume = {41},
-year = {2008}
-}
-@article{DAndrea2016,
-abstract = {Among approaches to establish the importance of niche differentiation for species coexistence, the use of functional traits is attractive for its potential to suggest specific coexistence mechanisms. Recent studies have looked for trait patterns reflective of niche differentiation, building on a line of research with a deep but somewhat neglected history. We review the field from its foundation in limiting similarity theory in the 1960s to its resurgence in 2000s, and find the theory of trait patterning still in a stage of development. Elements still to be accounted for include environmental fluctuations, multidimensional niche space, transient dynamics, immigration, intraspecific variation, evolution and spatial scales. Recent empirical methods are better than early approaches, but still focus on patterning arising in simplistic models, and should rigorously link niche space with trait space, use informative null models, and adopt new metrics of pattern as theory develops. Because tests based on overly simplistic expectations of trait pattern are of little value, we argue that progress in the field requires theory development, which should entail exploring patterns across a set of conceptual and system-specific models of competition along trait axes},
-author = {D'Andrea, Rafael and Ostling, Annette},
-doi = {10.1111/oik.02979},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/D'Andrea, Ostling - 2016 - Challenges in linking trait patterns to niche differentiation.pdf:pdf},
-journal = {Oikos},
-number = {10},
-pages = {1369--1385},
-title = {{Challenges in linking trait patterns to niche differentiation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/oik.02979/abstract},
-volume = {125},
-year = {2016}
-}
-@incollection{Goreaud1997,
-address = {Oeiras, Portugal},
-author = {Goreaud, Fran{\c{c}}ois and Courbaud, Beno{\^{i}}t and Collinet, Fr{\'{e}}d{\'{e}}rique},
-booktitle = {IUFRO Workshop: Empirical and process-based models for forest tree and stand growth simulation},
-editor = {Amaro, A and Tom{\'{e}}, M},
-pages = {155--172},
-publisher = {Novas Tecnologias},
-title = {{Spatial structure analysis applied to modelling of forest dynamics: a few examples}},
-year = {1997}
-}
-@article{Gulllison2001,
-abstract = {This paper describes the development of a spatially-explicit forest transition model for the Clyburn River Valley watershed in northern Cape Breton Island, Nova Scotia, Canada. The model links spatial quantities of available sunlight, degree-day accumulation and soil water content to the establishment and growth of individual tree and shrub species. Environment-species interactions are captured by way of an artificial neural network (ANN) trained to detect temporal patterns produced with a forest gap model (GIZELA) calibrated for environmental and forest species conditions encountered in northern Cape Breton Island. Impact of environmental conditions on forest succession is expressed through numerical adjustments of the ANN-produced forest-transition projections for several representative landscape types. The ANN-transition modelling approach used is largely automated, making it easy to apply at the species level. ANN calculations explain {\textgreater}95{\%} of the variation present in all GIZELA simulations. Forest-transition calculations are subsequently applied to a representative area of the Cape Breton Highlands as a demonstration of the landscape application of the ANN. Forest-transition modelling can aid in the understanding and prediction of natural forest succession at the landscape level, facilitating the development of long-term conservation plans. {\textcopyright} 2001 Elsevier Science B.V. All rights reserved.},
-author = {Gulllison, Jeremy J and Bourque, Charles P.-A.},
-doi = {10.1016/S0304-3800(00)00428-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gulllison, Bourque - 2001 - Spatial prediction of tree and shrub succession in a small watershed in Northern Cape Breton Island, Nova Sc.pdf:pdf},
-journal = {Ecological Modelling},
-number = {2-3},
-pages = {181--199},
-title = {{Spatial prediction of tree and shrub succession in a small watershed in Northern Cape Breton Island, Nova Scotia, Canada}},
-url = {http://www.sciencedirect.com/science/article/pii/S0304380000004282},
-volume = {137},
-year = {2001}
-}
-@article{Pavoine2015,
-abstract = {Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity. This change of perspective has a main objective: disentangling the processes that drive species distributions from local to broad scales. A fundamental difference between phylogenetic and functional analyses is that phylogeny is intrinsically dependent on a tree-like structure whereas functional data can, most of time, only be forced to adhere a tree structure, not without some loss of information. When the branches of a phylogenetic tree have lengths, then each evolutionary unit on these branches can be considered as a basic entity on which dissimilarities among sites should be measured. Several of the recent measures of phylogenetic dissimilarities among sites thus are traditional dissimilarity indices where species are replaced by evolutionary units. The resulting indices were named PD-dissimilarity indices, in reference to early work on the phylogenetic diversity (PD) measure. Here I review and compare indices and ordination approaches that, although first developed to analyse the differences in the species compositions of sites, can be adapted to describe PD-dissimilarities among sites. Using simulations of species distributions along environmental gradients, I compare indices, associated with permutation tests and null models, in their ability to reveal existing phylogenetic patterns along the gradients. As an illustration, I show that the amount of bat PD-dissimilarities along a disturbance gradient in Selva Lacandona of Chiapas, Mexico is dependent on whether species' abundance is considered, and on the PD-dissimilarity index used. Overall, the family of PD-dissimilarity indices has a critical potential for future analyses of phylogenetic diversity as it benefits from decades of research on the measure of species dissimilarity. I provide clues to help to choose among many potential indices, identifying which indices satisfy minimal basic properties, and analysing their sensitivity to abundance, size, diversity and joint absences.},
-author = {Pavoine, Sandrine},
-doi = {10.1111/oik.03262},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine - 2015 - A guide through a family of phylogenetic dissimilarity measures among sites.pdf:pdf},
-journal = {Oikos},
-title = {{A guide through a family of phylogenetic dissimilarity measures among sites}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/oik.03262/abstract},
-volume = {in press},
-year = {2016}
-}
-@article{Cadotte2017a,
-abstract = {The ability to explain why multispecies assemblages produce greater biomass compared to monocultures, has been a central goal in the quest to understand biodiversity effects on ecosystem function. Species contributions to ecosystem function can be driven by two processes: niche complementarity and a selection effect that is influenced by fitness (competitive) differences, and both can be approximated with measures of species' traits. It has been hypothesised that fitness differences are associated with few, singular traits while complementarity requires multidimensional trait measures. Here, using experimental data from plant assemblages, I show that the selection effect was strongest when trait dissimilarity was low, while complementarity was greatest with high trait dissimilarity. Selection effects were best explained by a single trait, plant height. Complementarity was correlated with dissimilarity across multiple traits, representing above and below ground processes. By identifying the relevant traits linked to ecosystem function, we obtain the ability to predict combinations of species that will maximise ecosystem function.},
-author = {Cadotte, Marc W.},
-doi = {10.1111/ele.12796},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte - 2017 - Functional traits explain ecosystem function through opposing mechanisms.pdf:pdf},
-journal = {Ecology Letters},
-number = {8},
-pages = {989--996},
-title = {{Functional traits explain ecosystem function through opposing mechanisms}},
-volume = {20},
-year = {2017}
-}
-@article{Chase2011,
-abstract = {$\beta$-diversity represents the compositional variation among communities from site-to-site, linking local ($\alpha$-diversity) and regional ($\gamma$-diversity). Researchers often desire to compare values of $\beta$-diversity across localities or experimental treatments, and to use this comparison to infer possible mechanisms of community assembly. However, the majority of metrics used to estimate $\beta$-diversity, including most dissimilarity metrics (e.g., Jaccard's and S{\o}renson's dissimilarity index), can vary simply because of changes in the other two diversity components ($\alpha$ or $\gamma$-diversity). Here, we overview the utility of taking a null model approach that allows one to discern whether variation in the measured dissimilarity among communities results more from changes in the underlying structure by which communities vary, or instead simply due to difference in $\alpha$-diversity among localities or experimental treatments. We illustrate one particular approach, originally developed by Raup and Crick (1979) in the paleontological litera...},
-author = {Chase, Jonathan M. and Kraft, Nathan J. B. and Smith, Kevin G. and Vellend, Mark and Inouye, Brian D},
-doi = {10.1890/ES10-00117.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chase et al. - 2011 - Using null models to disentangle variation in community dissimilarity from variation in $\alpha$-diversity.pdf:pdf},
-journal = {Ecosphere},
-number = {2},
-pages = {art. 24},
-title = {{Using null models to disentangle variation in community dissimilarity from variation in $\alpha$-diversity}},
-volume = {2},
-year = {2011}
-}
-@article{Arbia2016b,
-abstract = {Spatial econometrics can be defined in a narrow and in a broader sense. In a narrow sense it refers to methods and techniques for the analysis of regression models using data observed within discrete portions of space such as countries or regions. In a broader sense it is inclusive of the models and theoretical instruments of spatial statistics and spatial data analysis to analyze various economic effects such as externalities, interactions, spatial concentration and many others. Indeed, the reference methodology for spatial econometrics lies on the advances in spatial statistics where it is customary to distinguish between different typologies of data that can be encountered in empirical cases and that require different modelling strategies. A first distinction is between continuous spatial data and data observed on a discrete space. Continuous spatial data are very common in many scientific disciplines (such as physics and environmental sciences), but are still not currently considered in the spatial econometrics literature. Discrete spatial data can take the form of points, lines and polygons. Point data refer to the position of the single economic agent observed at an individual level. Lines in space take the form of interactions between two spatial locations such as flows of goods, individuals and information. Finally data observed within polygons can take the form of predefined irregular portions of space, usually administrative partitions such as countries, regions or counties within one country. In this monograph we will adopt a broader view of spatial econometrics and we will introduce some of the basic concepts and the fundamental distinctions needed to properly analyze economic datasets observed as points, regions or lines over space. It cannot be overlooked the fact that the mainstream spatial econometric literature was recently the subject for harsh and radical criticisms by a number of papers. The purpose of this monograph is to show that much of these criticisms are in fact well grounded, but that they lose relevance if we abandon the narrow paradigm of a discipline centered on the regression analysis of regional data, and we embrace the wider acceptation adopted here. In Section 2 we will introduce methods for the spatial econometric analysis of regional data that, so far, have been the workhorse of most theoretical and empirical work in the literature. We will consider modelling strategies falling within the general structure of the SARAR paradigm and its particularizations by presenting the various estimation and hypothesis testing procedures based on Maximum Likelihood (ML), Generalized Method of Moments (GMM) and Two-Stage Least Squares (2SLS), that were proposed in the literature to remove the ineffieciencies and inconsistencies arising from the presence of various forms of spatial dependence. Section 3 is devoted to the new emerging field of spatial econometric analysis of individual granular spatial data sometimes referred to as spatial microeconometrics. We present modelling strategies that use information about the actual position of each economic agent to explain both individuals' location decisions and the economic actions observed in the chosen locations. We will discuss the peculiarities of general spatial autoregressive model in this setting and the use of models where distances are used as predictors in a regression framework. We will also present some point pattern methods to model individuals' locational choices, as well as phenomena of co-localization and joint-localization. Finally in Section 4 the general SARAR paradigm is applied to the case of spatial interaction models estimated using data in the form of origin–destination variables and specified following models based on the analogy with the Newtonian law of universal gravitation. The discussion in this monograph is intentionally limited to the analysis of spatial data observed in a single moment of time leaving out of presentation the case of dynamic spatial data such as those observed in spatial panel data.},
-author = {Arbia, Giuseppe},
-doi = {10.1561/0800000030},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia - 2016 - Spatial Econometrics A Broad View.pdf:pdf},
-journal = {Foundations and Trends in Econometrics},
-number = {3-4},
-pages = {145--265},
-title = {{Spatial Econometrics : A Broad View}},
-url = {http://dx.doi.org/10.1561/0800000030},
-volume = {8},
-year = {2016}
-}
-@book{Fortin2005,
-address = {Cambridge },
-author = {Fortin, Marie-Jos{\'{e}}e and Dale, Mark R T},
-chapter = {365},
-publisher = {Cambridge University Press},
-title = {{Spatial Analysis. A guide for ecologists.}},
-year = {2005}
-}
-@article{Geary1954,
-abstract = {The problem discussed in this paper is to determine whether statistics given for each "county" in a "country" are distributed at random or whether they form a pattern.},
-author = {Geary, R .C.},
-doi = {10.2307/2986645},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Geary - 1954 - The contiguity ratio and statistical mapping.pdf:pdf},
-journal = {The Incorporated Statistician},
-number = {3},
-pages = {115--145},
-title = {{The contiguity ratio and statistical mapping}},
-url = {https://www.jstor.org/stable/2986645},
-volume = {5},
-year = {1954}
-}
-@book{Cochran1992,
-address = {New York},
-author = {Cochran, William G. and Cox, Gertrude M.},
-edition = {2nd ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cochran, Cox - 1992 - Experimental Designs.pdf:pdf},
-publisher = {John Wiley {\&} Sons},
-title = {{Experimental Designs}},
-year = {1992}
-}
-@article{Harte2013,
-abstract = {A theory of macroecology based on the maximum information entropy (MaxEnt) inference procedure predicts that the log-log slope of the species-area relationship (SAR) at any spatial scale is a specified function of the ratio of abundance, N(A), to species richness, S(A), at that scale. The theory thus predicts, in generally good agreement with observation, that all SARs collapse onto a specified universal curve when local slope, z(A), is plotted against N(A)/S(A). A recent publication, however, argues that if it is assumed that patterns in macroecology are independent of the taxonomic choices that define assemblages of species, then this principle of "taxon invariance" precludes the MaxEnt-predicted universality of the SAR. By distinguishing two dimensions of the notion of taxon invariance, we show that while the MaxEnt-based theory predicts universality regardless of the taxonomic choices that define an assemblage of species, the biological characteristics of assemblages should under MaxEnt, and do in reality, influence the realism of the predictions.},
-author = {Harte, John and Kitzes, Justin and Newman, Erica A. and Rominger, Andrew J.},
-doi = {10.1086/668821},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harte et al. - 2013 - Taxon categories and the universal species-area relationship (a comment on {\v{S}}izling et al., “between geometry and b.pdf:pdf},
-journal = {The American naturalist},
-number = {2},
-pages = {282--287},
-title = {{Taxon categories and the universal species-area relationship (a comment on {\v{S}}izling et al., “between geometry and biology:the problem of universality of the species-area relationship”).}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/23348782},
-volume = {181},
-year = {2013}
-}
-@article{Villeger2008,
-abstract = {1. The distribution of biodiversity at multiple spatial scales has been traditionally investigated through the additive partitioning of gamma-biodiversity (regional) into alpha-(within-site) and beta-(among-site) components. 2. However, this decomposition is almost exclusively applied using species turnover among communities while two communities with no species in common can be very similar because they share some 'biological' similarity. 3. To overcome this limitation, Hardy {\&} Senterre (2007) (J. Ecol., 95, 493-506) presented a new statistical framework partitioning the phylogenetic diversity into alpha- and beta-components using the Rao's quadratic entropy. 4. We show that their decomposition is correct only when sites have the same total abundance, otherwise it may lead to negative beta-diversity values. As an alternative, we provided a general decomposition of the quadratic entropy into alpha-, beta- and gamma-diversities. 5. Synthesis. We suggest that the 'biological' turnover quantified by the beta-component of the regional quadratic entropy may help, at least, to disentangle dispersal vs. niche influences on biodiversity patterns.},
-annote = {Villeger, Sebastien Mouillot, David},
-author = {Vill{\'{e}}ger, S{\'{e}}bastien and Mouillot, David},
-doi = {10.1111/j.1365-2745.2007.01351.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vill{\'{e}}ger, Mouillot - 2008 - Additive partitioning of diversity including species differences a comment on Hardy {\&} Senterre (2007).pdf:pdf},
-journal = {Journal of Ecology},
-number = {5},
-pages = {845--848},
-title = {{Additive partitioning of diversity including species differences: a comment on Hardy {\&} Senterre (2007)}},
-volume = {96},
-year = {2008}
-}
-@article{Bade2015,
-abstract = {We show that key functions are spatially clustered with, or dispersed from, each other even within manufacturing industries in West Germany, and that these clustering or dispersion patterns have changed significantly during recent decades. Estimating levels and changes (1992–2007) of localizations and colocalizations of selected functions (production, headquarter services, R{\&}D) within 27 West German industriesbymeans of K densities,weidentify twobroad groups of industries. In “frag- menting” industries, which account for half of manufacturing employment, functions were more clustered with each other than the industry as a whole after the fall of the Iron Curtain but have, in accordance with regional theories of spatial fragmentation, been unbundled spatially from each other subsequently. In “integrating” industries, by contrast, which account for one-third of manufacturing employment, functions were initially dispersed from each other but have subsequently been rebundled spatially with each other. This spatial rebundling may be a consequence of offshoring, i.e., international fragmentation.},
-author = {Bade, Franz-Josef and Bode, Eckhardt and Cutrini, Eleonora},
-doi = {10.1007/s00168-014-0652-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bade, Bode, Cutrini - 2015 - Spatial fragmentation of industries by functions.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {1},
-pages = {215--250},
-title = {{Spatial fragmentation of industries by functions}},
-url = {http://link.springer.com/10.1007/s00168-014-0652-y},
-volume = {54},
-year = {2015}
-}
-@incollection{Holmes2004,
-address = {Amsterdam},
-author = {Holmes, Thomas J. and Stevens, John J.},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holmes, Stevens - 2004 - Spatial Distribution of Economic Activities in North America.pdf:pdf},
-keywords = {Holmes (2003).pdf},
-mendeley-tags = {Holmes (2003).pdf},
-publisher = {Elsevier. North Holland},
-title = {{Spatial Distribution of Economic Activities in North America}},
-year = {2004}
-}
-@article{Yguel2016,
-abstract = {Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Herewe propose a newmetric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the “ELDERness surfaces.” These parameters captured variation in productivity of a grassland com- munity better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots)weremore productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.},
-author = {Yguel, Benjamin and Jactel, Herv{\'{e}} and Pearse, Ian S. and Moen, Daniel and Winter, Marten and Hortal, Joaquin and Helmus, Matthew R. and K{\"{u}}hn, Ingolf and Pavoine, Sandrine and Purschke, Oliver and Weiher, Evan and Violle, Cyrille and Ozinga, Wim and Br{\"{a}}ndle, Martin and Bartish, Igor V. and Prinzing, Andreas},
-doi = {10.1086/687964},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Yguel et al. - 2016 - The Evolutionary Legacy of Diversification Predicts Ecosystem Function.pdf:pdf},
-journal = {The American Naturalist},
-number = {4},
-pages = {398--410},
-title = {{The Evolutionary Legacy of Diversification Predicts Ecosystem Function}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/687964},
-volume = {188},
-year = {2016}
-}
-@article{Eddelbuettel2011,
-abstract = {The Rcpp package simplifies integrating C++ code with R. It provides a consistent C++ class hierarchy that maps various types of R objects (vectors, matrices, functions, environments, . . . ) to dedicated C++ classes. Object interchange between R and C++ is managed by simple, flexible and extensible concepts which include broad support for C++ Standard Template Library idioms. C++ code can both be compiled, linked and loaded on the fly, or added via packages. Flexible error and exception code handling is provided. Rcpp substantially lowers the barrier for programmers wanting to combine C++ code with R.},
-author = {Eddelbuettel, Dirk and Fran{\c{c}}ois, Romain},
-doi = {10.18637/jss.v040.i08},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eddelbuettel, Fran{\c{c}}ois - 2011 - Rcpp Seamless R and C Integration.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {8},
-pages = {1--18},
-title = {{Rcpp: Seamless R and C++ Integration}},
-url = {http://www.jstatsoft.org/v40/i08/},
-volume = {40},
-year = {2011}
-}
-@article{Mason2003,
-abstract = {Functional diversity has been seen as the key to predicting the stability. invasibility, resource capture, nutrient cycling and productivity of communities. However, it has been unclear how to estimate it. Ten criteria for an index of functional diversity are developed. These include that it should reflect the range of characters present and the abundance of the species with those characters in the community, and be unaffected by the measurement units used or by the number of species. An index that meets all ten criteria, FDvar, is investigated. It is based on the variance in characters, weighted by the abundance of the species with those characters. Tested with artificial and randomly generated data, it showed reasonable use of the 0 - 1 range (mean 0.60, range 0.0009 - 0.975) and intuitive behaviour. Tested with field data from eight sites in New Zealand. it gave a good spread of values (mean 0.65, range across sites 0.34 - 0.84). showed good ability to distinguish between the communities and its performance was ecologically intuitive. Illustrative correlations are made with mean annual temperature and soil fertility, determined by a bio-assay. FDvar is recommended for general use.},
-author = {Mason, Norman W. H. and MacGillivray, Kit and Steel, John B. and Wilson, J. Bastow},
-doi = {10.1111/j.1654-1103.2003.tb02184.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mason et al. - 2003 - An index of functional diversity.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {571--578},
-title = {{An index of functional diversity}},
-volume = {14},
-year = {2003}
-}
-@article{Guan2008a,
-abstract = {We introduce a formal testing procedure to assess the fit of an inhomogeneous spatial Poisson process model, based on a discrepancy measure function that is constructed from residuals obtained from the fitted model. We derive the asymptotic distributional properties of and develop a test statistic based on them. Our test statistic has a limiting standard normal distribution, so that the test can be performed by simply comparing the test statistic with readily available critical values. We perform a simulation study to assess the performance of the proposed method and apply it to a real data example. {\textcopyright} 2008 Biometrika Trust.},
-annote = {cited By (since 1996) 0},
-author = {Guan, Yontao},
-doi = {10.1093/biomet/asn045},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2008 - A goodness-of-fit test for inhomogeneous spatial Poisson processes.pdf:pdf},
-journal = {Biometrika},
-number = {4},
-pages = {831--845},
-title = {{A goodness-of-fit test for inhomogeneous spatial Poisson processes}},
-volume = {95},
-year = {2008}
-}
-@article{Scheffer2006,
-abstract = {Ecologists have long been puzzled by the fact that there are so many similar species in nature. Here we show that self-organized clusters of look-a-likes may emerge spontaneously from coevolution of competitors. The explanation is that there are two alternative ways to survive together: being sufficiently different or being sufficiently similar. Using a model based on classical competition theory, we demonstrate a tendency for evolutionary emergence of regularly spaced lumps of similar species along a niche axis. Indeed, such lumpy patterns are commonly observed in size distributions of organisms ranging from algae, zooplankton, and beetles to birds and mammals, and could not be well explained by earlier theory. Our results suggest that these patterns may represent self-constructed niches emerging from competitive interactions. A corollary of our findings is that, whereas in species-poor communities sympatric speciation and invasion of open niches is possible, species-saturated communities may be characterized by convergent evolution and invasion by look-a-likes.},
-author = {Scheffer, M. and van Nes, E. H.},
-doi = {10.1073/pnas.0508024103},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheffer, van Nes - 2006 - Self-organized similarity, the evolutionary emergence of groups of similar species.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {16},
-pages = {6230--6235},
-title = {{Self-organized similarity, the evolutionary emergence of groups of similar species}},
-url = {http://www.pnas.org/content/103/16/6230},
-volume = {103},
-year = {2006}
-}
-@article{Purschke2013,
-abstract = {1. Theory predicts that the processes generating biodiversity after disturbance will change during suc-cession. Comparisons of phylogenetic and functional (alpha and beta) diversity with taxonomic diver-sity can provide insights into the extent to which community assembly is driven by deterministic or stochastic processes, but comparative approaches have yet to be applied to successional systems. 2. We characterized taxonomic, phylogenetic and functional plant (alpha and beta) diversity within and between four successional stages in a {\textgreater} 270-year-long arable-to-grassland chronosequence. Null models were used to test whether functional and phylogenetic turnover differed from random expec-tations, given the levels of species diversity. 3. The three facets of diversity showed different patterns of change during succession. Between early and early-mid succession, species richness increased but there was no increase in functional or phylogenetic diversity. Higher than predicted levels of functional similarity between species within the early and early-mid successional stages, indicate that abiotic filters have selected for sets of func-tionally similar species within sites. Between late-mid and late succession, there was no further increase in species richness, but a significant increase in functional alpha diversity, suggesting that functionally redundant species were replaced by functionally more dissimilar species. Functional turnover between stages was higher than predicted, and higher than within-stage turnover, indicating that different assembly processes act at different successional stages. 4. Synthesis. Analysis of spatial and temporal turnover in different facets of diversity suggests that deterministic processes generate biodiversity during post-disturbance ecosystem development and that the relative importance of assembly processes has changed over time. Trait-mediated abiotic fil-tering appears to play an important role in community assembly during the early and early-mid stages of arable-to-grassland succession, whereas the relative importance of competitive exclusion appears to have increased towards the later successional stages. Phylogenetic diversity provided a poor reflection of functional diversity and did not contribute to inferences about underlying assembly processes. Functionally deterministic assembly suggests that it may be possible to predict future post-disturbance changes in biodiversity, and associated ecosystem attributes, on the basis of spe-cies' functional traits but not phylogeny.},
-author = {Purschke, Oliver and Schmid, Barbara C. and Sykes, Martin T. and Poschlod, Peter and Michalski, Stefan G. and Durka, Walter and K{\"{u}}hn, Ingolf and Winter, Marten and Prentice, Honor C.},
-doi = {10.1111/1365-2745.12098},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Purschke et al. - 2013 - Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession Insights.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {857--866},
-title = {{Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession: Insights into assembly processes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12098/abstract},
-volume = {101},
-year = {2013}
-}
-@incollection{Engen1979,
-address = {Fairland, MD},
-author = {Engen, Steinar},
-booktitle = {Ecological Diversity in Theory and Practice},
-editor = {Grassle, J. Frederick and Patil, Ganapati P. and Smith, W. K. and Taillie, Charles},
-pages = {37--50},
-publisher = {International Cooperative Publishing House},
-title = {{Some basic concepts of ecological equitability}},
-year = {1979}
-}
-@article{Mendes2008,
-abstract = {Several indices have been created to measure diversity, and the most frequently used are the Shannon-Wiener (H) and Simpson (D) indices along with the number of species (S) and evenness (E). Controversies about which index should be used are common in literature. However, a generalized entropy (Tsallis entropy) has the potential to solve part of these problems. Here we explore a family of diversity indices (S-q; where q is the Tsallis index) and evenness (E-q), based on Tsallis entropy that incorporates the most used indices. It approaches S when q=0, H when q -{\textgreater} 1 and gives D when q=2. In general, varying the value of the Tsallis index (q), S-q varies from emphasis on species richness (q {\textless} 1) to emphasis on dominance (q {\textgreater} 1). Similarly, E-q also works as a tool to investigate diversity. In particular, for a given community, its minimum value represents the maximum deviation from homogeneity (E-q=1) for a particular q (herein named q*). It is remarkable that our analysis indicates that q* and its corresponding evenness, E-q*, are negatively affected by S when using simulated data. They may represent an index related to species rarity. Furthermore, S-q* (i.e. the value of S-q for a specific q*) is positively affected by richness that is an important property of any diversity index. In general, our findings indicate that the indices H, D, S, S-q*, E and E-q* are only part of a whole set of possibilities. In addition, the ecological properties of E-q* and S-q*, proposed here for the first time, show promise in ecology.},
-annote = {Mendes, Renio S. Evangelista, Luiz R. Thomaz, Sidinei M. Agostinho, Angelo A. Gomes, Luiz C.},
-author = {Mendes, R. S. and Evangelista, L. R. and Thomaz, S. M. and Agostinho, A. A. and Gomes, L. C.},
-doi = {10.1111/j.0906-7590.2008.05469.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mendes et al. - 2008 - A unified index to measure ecological diversity and species rarity.pdf:pdf},
-journal = {Ecography},
-number = {4},
-pages = {450--456},
-title = {{A unified index to measure ecological diversity and species rarity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2008.05469.x/abstract},
-volume = {31},
-year = {2008}
-}
-@article{Smith2013,
-abstract = {Phenotypic traits mediate organisms' interactions with the environment and determine how they affect and are affected by their biotic and abiotic milieu. Thus, dispersion of trait values, or functional diversity (FD) of a community can offer insights into processes driving community assembly. For example, underdispersion of FD suggests that habitat “filtering” of species with unfavorable trait values restricts the species that can exist in a particular habitat, while even spacing of FD suggests that interspecific competition, or biotic “sorting,” discourages the coexistence of species with similar trait values. Since assembly processes are expected to vary as a function of spatial scale, we should also expect patterns of FD to reflect scale dependence in filtering and biotic sorting. Here we present the concept of the functional-diversity–area relationship (FAR), which is similar to the species–area relationship but plots a measure of phenotypic trait diversity as a function of spatial scale. We develop a set of null model tests that discriminate between FARs generated predominantly by filtering or biotic sorting and indicate the scales at which these effects are pronounced. The utility of the FAR for addressing long-standing issues in ecology is illustrated with several examples. A multi-scale examination of FD and its pattern relative to null expectations provides an important tool for ecologists interested in understanding the scale dependence of community assembly processes.},
-author = {Smith, Adam B. and Sandel, Brody and Kraft, Nathan J. B. and Carey, Susan},
-doi = {10.1890/12-2109.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith et al. - 2013 - Characterizing scale-dependent community assembly using the functinoal-diversity-area relationship.pdf:pdf},
-journal = {Ecology},
-number = {11},
-pages = {2392--2402},
-title = {{Characterizing scale-dependent community assembly using the functinoal-diversity-area relationship}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/12-2109.1/abstract},
-volume = {94},
-year = {2013}
-}
-@article{Evangelista2009,
-abstract = {A family of entropy indices constructed in the framework of Tsallis entropy formalism is used to investigate ecological diversity. It represents a new perspective in ecology because a simple equation can incorporate all aspects of $\alpha$−diversity, from richness to dominance and can be also related to a measure of species rarity. In addition, a generalized Kullback-Leibler distance, constructed in the framework of a nonextensive formalism, is recalled and used as a measure of $\beta$−diversity between two systems. These tools are applied to data relative to the macrophytes collected from two not far apart arms of Itaipu Reservoir, in Parana River basin.},
-author = {Evangelista, H. B. A. and Thomaz, S. M. and Mendes, R. S. and Evangelista, L. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Evangelista et al. - 2009 - Generalized entropy indices to measure $\alpha$- and $\beta$-diversities of macrophytes.pdf:pdf},
-isbn = {0103-9733},
-journal = {Brazilian Journal of Physics},
-pages = {369--401},
-title = {{Generalized entropy indices to measure $\alpha$- and $\beta$-diversities of macrophytes}},
-url = {http://www.scielo.br/scielo.php?script=sci{\_}arttext{\&}pid=S0103-97332009000400008{\&}nrm=iso},
-volume = {39},
-year = {2009}
-}
-@article{Dunning1988,
-author = {Dunning, J. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dunning - 1988 - The Determinants of International Production.pdf:pdf},
-journal = {Oxford Economic Papers},
-number = {3},
-pages = {289--336},
-title = {{The Determinants of International Production}},
-url = {https://www.jstor.org/stable/2662317},
-volume = {25},
-year = {1988}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2002,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n°2002-634 du 29 avril 2002 portant cr{\'{e}}ation du compte {\'{e}}pargne-temps dans la fonction publique de l'Etat et dans la magistrature.}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000590403},
-year = {2002}
-}
-@article{Crozet2004,
-abstract = {This paper studies the determinants of location choice by foreign investors in France using a sample of almost 4000 foreign investments over 10 years and 92 locations. Concerning agglomeration effects, we find very strong evidence of positive spillovers between firms, and identify detailed patterns of clustering, assessing, for instance, the countries of origin and the industries for which those spillovers are the most substantial. Concerning regional policies, we find very little evidence of any positive impact. Finally, we identify a ‘learning process' of FDI, the location decisions becoming more remote from the country of origin during the period we study.},
-author = {Crozet, Mathieu and Mayer, Thierry and Mucchielli, Jean-Louis},
-doi = {10.1016/S0166-0462(03)00010-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Crozet, Mayer, Mucchielli - 2004 - How do firms agglomerate A study of FDI in France.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {1},
-pages = {27-- 54},
-title = {{How do firms agglomerate? A study of FDI in France}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046203000103},
-volume = {34},
-year = {2004}
-}
-@article{Dray2003,
-abstract = {Ecological studies often require studying the common structure of a pair of data tables. Co-inertia analysis is a multivariate method for coupling two tables. It is often neglected by ecologists who prefer the widely used methods of redundancy analysis and canonical correspondence analysis. We present the co-inertia criterion for measuring the adequacy between two data sets. Co-inertia analysis is based on this criterion as are canonical correspondence analysis or canonical correlation analysis, but the latter two have additional constraints. Co-inertia analysis is very flexible and allows many possibilities for coupling. Co-inertia analysis is suitable for quantitative and/or qualitative or fuzzy environmental variables. Moreover, various weighting of sites and various transformations and/or centering of species data are available for this method. Hence, more ecological considerations can be taken into account in the statistical procedures. Moreover, the principle of this method is very general and can be easily extended to the case of distance matrices or to the case of more than two tables. Simulated ecological data are used to compare the co-inertia approach with other available methods.},
-author = {Dray, St{\'{e}}phane and Chessel, Daniel and Thioulouse, Jean},
-doi = {10.1890/03-0178},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dray, Chessel, Thioulouse - 2003 - Co-inertia analysis and the linking of ecological data tables.pdf:pdf},
-journal = {Ecology},
-number = {11},
-pages = {3078--3089},
-title = {{Co-Inertia Analysis and the Linking of Ecological Data Tables}},
-url = {http://www.esajournals.org/doi/abs/10.1890/03-0178},
-volume = {84},
-year = {2003}
-}
-@article{Alonso-Villar2012,
-abstract = {This paper first reflects on the concentration invariance property that regional economics implicitly assumes when the locational Gini index and the generalized entropy family of concentration indexes are used. Second, it suggests that apart from these indexes, concentration measures based on other inequality notions can be used as well. Thus, this paper proposes a variance-type concentration index and a Lorenz-type dominance criterion that are based on an alternative invariance condition. The use of several invariance notions allows for the exploration of concentration from different angles, which adds robustness to the results, as illustrated by using manufacturing employment data from Spain. {\textcopyright} 2012 Copyright Regional Studies Association.},
-annote = {Cited By (since 1996): 1
-Export Date: 15 May 2012
-Source: Scopus
-Language of Original Document: English; French; Spanish
-Correspondence Address: Alonso-Villar, O.; Departamento de Econom{\'{i}}a Aplicada, Facultade de CC. Econ{\'{o}}micas, Universidade de Vigo, Campus Lagoas-Marcosende s/n, Vigo, 36310, Spain; email: ovillar@uvigo.es},
-author = {Alonso-Villar, Olga and {Del R{\'{i}}o}, Coral},
-doi = {10.1080/17421772.2012.669494},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alonso-Villar, Del R{\'{i}}o - 2012 - Concentration of economic activity Inequality-based measures.pdf:pdf},
-journal = {Spatial Economic Analysis},
-number = {2},
-pages = {223--246},
-title = {{Concentration of economic activity: Inequality-based measures}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84860343876{\&}partnerID=40{\&}md5=4070025b84d6e952b08b6469a52a907e},
-volume = {7},
-year = {2012}
-}
-@article{Cowell1981,
-abstract = {The theory of inequality measurement is examined using some basic axioms which extend the Pigou/Dalton principle of transfers. From these basic axioms various inequality indices may be derived as an alternative to ad hoc methods, or to methods involving prior specification of a social welfare function. The key idea is the concept of `distance' between two income shares. Conventional inequality indices are analysed in terms of their implied distance functions.},
-author = {Cowell, Frank A. and Kuga, Kiyoshi},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cowell, Kuga - 1981 - Inequality measurement An axiomatic approach.pdf:pdf},
-journal = {European Economic Review},
-number = {3},
-pages = {287--305},
-title = {{Inequality measurement: An axiomatic approach}},
-url = {http://www.sciencedirect.com/science/article/B6V64-4NC3BMG-3/2/a014cc4b78a21be19e9e054e40156f21},
-volume = {15},
-year = {1981}
-}
-@article{EhrlichP.R.andRaven1964,
-author = {{Ehrlich, P. R. and Raven}, P. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ehrlich, P. R. and Raven - 1964 - Butterflies and Plants A Study in Coevolution.pdf:pdf},
-journal = {Evolution},
-number = {4},
-pages = {586--608},
-title = {{Butterflies and Plants : A Study in Coevolution}},
-volume = {18},
-year = {1964}
-}
-@article{Clavel2013,
-abstract = {Biodiversity has reached a critical state. In this context, stakeholders need indicators that both provide a synthetic view of the state of biodiversity and can be used as communication tools. Using river fishes as model, we developed community indicators that aim at integrating various components of biodiversity including interactions between species and ultimately the processes influencing ecosystem functions. We developed indices at the species level based on (i) the concept of specialization directly linked to the niche theory and (ii) the concept of originality measuring the overall degree of differences between a species and all other species in the same clade. Five major types of originality indices, based on phylogeny, habitat-linked and diet-linked morphology, life history traits, and ecological niche were analyzed. In a second step, we tested the relationship between all biodiversity indices and land use as a proxy of human pressures. Fish communities showed no significant temporal trend for most of these indices, but both originality indices based on diet- and habitat- linked morphology showed a significant increase through time. From a spatial point of view, all indices clearly singled out Corsica Island as having higher average originality and specialization. Finally, we observed that the originality index based on niche traits might be used as an informative biodiversity indicator because we showed it is sensitive to different land use classes along a landscape artificialization gradient. Moreover, its response remained unchanged over two other land use classifications at the global scale and also at the regional scale.},
-author = {Clavel, Joanne and Poulet, Nicolas and Porcher, Emmanuelle and Blanchet, Simon and Grenouillet, Ga{\"{e}}l and Pavoine, Sandrine and Biton, Anne and Seon-Massin, Nirmala and Argillier, Christine and Daufresne, Martin and Teillac-Deschamps, Pauline and Julliard, Romain},
-doi = {10.1371/journal.pone.0080968},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clavel et al. - 2013 - A New Freshwater Biodiversity Indicator Based on Fish Community Assemblages.pdf:pdf},
-journal = {Plos One},
-number = {11},
-pages = {e80968},
-title = {{A New Freshwater Biodiversity Indicator Based on Fish Community Assemblages}},
-url = {http://dx.doi.org/10.1371{\%}2Fjournal.pone.0080968},
-volume = {8},
-year = {2013}
-}
-@techreport{Gerard1998,
-author = {G{\'{e}}rard, J. and {Edi Kouassi}, A. and Daigremont, C. and D{\'{e}}tienne, P. and Fouquet, D. and Vernay, M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/G{\'{e}}rard et al. - 1998 - Synth{\`{e}}se sur les caract{\'{e}}ristiques technologiques de r{\'{e}}f{\'{e}}rence des principaux bois commerciaux africains.pdf:pdf},
-publisher = {CIRAD-For{\^{e}}t},
-title = {{Synth{\`{e}}se sur les caract{\'{e}}ristiques technologiques de r{\'{e}}f{\'{e}}rence des principaux bois commerciaux africains}},
-year = {1998}
-}
-@book{Balee2013,
-abstract = {Cultural Forests of the Amazon is a comprehensive and diverse account of how indigenous people transformed landscapes and managed resources in the most extensive region of tropical forests in the world. Until recently, most scholars and scientists, as well as the general public, thought indigenous people had a minimal impact on Amazon forests, once considered to be total wildernesses. William Bal{\'{e}}e's research, conducted over a span of three decades, shows a more complicated truth. In Cultural Forests of the Amazon, he argues that indigenous people,},
-address = {Tuscaloosa, Alabama},
-author = {Bal{\'{e}}e, William},
-doi = {10.1111/aman.12194},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bal{\'{e}}e - 2013 - Cultural Forests of the Amazon A Historical Ecology of People and Their Landscapes.pdf:pdf},
-isbn = {9780817317867},
-publisher = {The University of Alabama Press},
-title = {{Cultural Forests of the Amazon: A Historical Ecology of People and Their Landscapes}},
-year = {2013}
-}
-@article{Dube2014a,
-author = {Dub{\'{e}}, Jean and Brunelle, C{\'{e}}dric},
-doi = {10.1007/s00168-014-0627-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dub{\'{e}}, Brunelle - 2014 - Dots to dots a general methodology to build local indicators using spatial micro-data.pdf:pdf},
-issn = {0570-1864},
-journal = {The Annals of Regional Science},
-month = {aug},
-number = {1},
-pages = {245--272},
-title = {{Dots to dots: a general methodology to build local indicators using spatial micro-data}},
-url = {http://link.springer.com/10.1007/s00168-014-0627-z},
-volume = {53},
-year = {2014}
-}
-@article{Edington1972,
-abstract = {(1) The investigation seeks to account for the coexistence, during the breeding season, of a number of similar bird species in a broad-leaved woodland. (2) Most species in the groups studied were separated spatially from one another, either horizontally or vertically. The horizontal separation took the form of mutually exclusive territories (wood warbler and willow warbler) or mutually exclusive feeding areas (e.g. tits, redstart and pied flycatcher). The vertical separation involved the use of different feeding zones. (3) Some of those species which were not separated spatially are specialized to take different foods. The temporal separation of breeding periods appears to be linked with food specializations. (4) It is argued that the spatial separation of species is largely a result of behavioural and morphological specializations which equip each species to locate and utilize particular parts of the wood. (5) Each season competitive interactions occurred between species. These influenced distribution patterns but the progressive displacement of any species seemed to be prevented by each species having a physical refuge. (6) In this wood the supply of nest-holes did not appear to be important in restricting the numbers or distribution of species. (7) The spatial separation of species had the effect of dividing the food resources in the wood either by separating foods according to type, or by the division of a single food resource into units. The ultimate significance of spatial patterns may lie in this subdivision of food resources. (8) Although it is theoretically possible for species to coexist when using the same food and without spatial separation, no example of this was found in the present study. (9) In investigations concerned with the coexistence of similar species in the same general habitat, the value of analysing spatial distribution patterns is emphasized.},
-author = {Edington, J. M. and Edington, M. A.},
-doi = {10.2307/3472},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Edington, Edington - 1972 - Spatial Patterns and Habitat Partition in the Breeding Birds of an Upland Wood.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {2},
-pages = {331--357},
-title = {{Spatial Patterns and Habitat Partition in the Breeding Birds of an Upland Wood}},
-url = {https://www.jstor.org/stable/3472},
-volume = {41},
-year = {1972}
-}
-@article{Pavoine2007,
-abstract = {Background: The development of post-genomic methods has dramatically increased the amount of qualitative and quantitative data available to understand how ecological complexity is shaped. Yet, new statistical tools are needed to use these data efficiently. In support of sequence analysis, diversity indices were developed to take into account both the relative frequencies of alleles and their genetic divergence. Furthermore, a method for describing inter-population nucleotide diversity has recently been proposed and named the double principal coordinate analysis (DPCoA), but this procedure can only be used with one locus. In order to tackle the problem of measuring and describing nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis. Results: This combination of methods allows i) testing and describing differences in patterns of inter-population diversity among loci, and ii) defining the best compromise among loci. These methods are illustrated by the analysis of both simulated data sets, which include ten loci evolving under a stepping stone model and a locus evolving under an alternative population structure, and a real data set focusing on the genetic structure of two nitrogen fixing bacteria, which is influenced by geographical isolation and host specialization. All programs needed to perform multiple DPCoA are freely available. Conclusion: Multiple DPCoA allows the evaluation of the impact of various loci in the measurement and description of diversity. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity.},
-author = {Pavoine, Sandrine and Bailly, Xavier},
-doi = {10.1186/1471-2148-7-156},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Bailly - 2007 - New analysis for consistency among markers in the study of genetic diversity development and application to the.pdf:pdf},
-journal = {BMC Evolutionary Biology},
-pages = {156},
-title = {{New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity}},
-volume = {7},
-year = {2007}
-}
-@article{Gregorius2016,
-abstract = {Admissible measures of diversity allow specification of the number of types (species, alleles, etc.) that are “effectively” involved in producing the diversity (the “diversity effective number”, also referred to as “true diversity”) of a community or population. In metacommunities, effective numbers additionally serve in partitioning the total diversity (symbolized by $\gamma$) into one component summarizing the diversity within communities (symbolized by $\alpha$) and an independent component summarizing the differences between communities (symbolized by $\beta$). There is growing consensus that the $\beta$-component should be treated in terms of an effective number of “distinct” communities in the metacommunity. Yet, the notion of distinctness is shown in the present paper to remain conceptually ambiguous at least with respect to the diversity within the “distinct” communities. To overcome this ambiguity and to provide the means for designing further desirable effective numbers, a new approach is taken that involves a generalized concept of effective number. The approach relies on first specifying the distributional characteristics of partitioning diversity among communities (among which are differentiation, where the same types tend to occur in the same communities, and apportionment, where different types tend to occur in different communities), then developing the indices which measure these characteristics, and finally inferring the effective numbers from these indices. Major results: (1) The $\beta$-component reflects apportionment characteristics of metacommunity structure and is quantified by the “apportionment effective number” of communities (number of effectively monomorphic communities). Since differentiation between communities arises only as a side effect of apportionment, the common interpretation of the $\beta$-component in terms of differentiation is unwarranted. (2) Multiplicative as well as additive methods of partitioning the total type diversity ($\gamma$) involve apportionment effective numbers of communities that are based on different apportionment indices. (3) “Differentiation effective numbers” of communities exist but do not conform with the classical concept of partitioning total type diversity into components within and between communities. (4) Differentiation characteristics are measured as effective numbers of distinct types (rather than communities) from the dual perspective, in which the roles of type and community membership are exchanged. This is relevant e.g. in studies of endemism and competitive exclusion. (5) For Shannon-Wiener diversity, all of the differentiation and apportionment effective numbers are equal, with the exception of those representing additive partitioning. (6) Under either perspective, that is dual or non-dual, measures of compositional differentiation (as originally suggested for the assessment of $\beta$-diversity) do not figure in the partitioning of total diversity into components, since they do not build on the intrinsic concept of diversity.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.1016/j.jtbi.2016.08.037},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 2016 - Effective numbers in the partitioning of biological diversity.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-pages = {133--147},
-title = {{Effective numbers in the partitioning of biological diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S002251931630279X},
-volume = {409},
-year = {2016}
-}
-@article{Perrin2000,
-abstract = {Recently, a model for non-stationary random field , n 2 has been developed. This consists of reducing Z to stationarity and isotropy via a bijective bi-differentiable deformation $\Phi$ of the index space. We give the form of this deformation under smoothness assumptions on the correlation of Z .},
-author = {Perrin, Olivier and Senoussi, Rachid},
-doi = {10.1016/S0167-7152(99)00188-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Perrin, Senoussi - 2000 - Reducing non-stationary random fields to stationarity and isotropy using a space deformation.pdf:pdf},
-journal = {Statistics {\&} Probability Letters},
-number = {1},
-pages = {23--32},
-title = {{Reducing non-stationary random fields to stationarity and isotropy using a space deformation}},
-url = {http://www.sciencedirect.com/science/article/pii/S0167715299001881},
-volume = {48},
-year = {2000}
-}
-@article{Furuichi2006,
-abstract = {A chain rule and a subadditivity for the entropy of type $\beta$, which is one of the nonadditive entropies, were derived by Z.Dar´ oczy. In this paper, we study the further relations among Tsallis type entropies which are typical nonadditive entropies. The chain rule is generalized by showing it for Tsallis relative entropy and the nonadditive entropy. We show some inequalities related to Tsallis entropies, especially the strong subadditivity for Tsallis type entropies and the subadditivity for the nonadditive entropies. The subadditivity and the strong subadditivity naturally lead to define Tsallis mutual entropy and Tsallis conditional mutual entropy, respectively, and then we show again chain rules for Tsallis mutual entropies. We give properties of entropic distances in terms of Tsallis entropies. Finally we show parametrically extended results based on information theory.},
-author = {Furuichi, Shigeru},
-doi = {10.1063/1.2165744},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Furuichi - 2006 - Information theoretical properties of Tsallis entropies.pdf:pdf},
-journal = {Journal of Mathematical Physics},
-number = {2},
-pages = {23302},
-title = {{Information theoretical properties of Tsallis entropies}},
-url = {http://dx.doi.org/10.1063/1.2165744},
-volume = {47},
-year = {2006}
-}
-@article{DeBello2016,
-abstract = {While an increasing number of indices for estimating the functional trait diversity of biological communities are being proposed, there is a growing demand by ecologists to clarify their actual implications and simplify index selection. Several key indices relate to mean trait dissimilarity between species within biological communities. Among them, the most widely used include (a) the mean species pairwise dissimilarity (MPD) and (b) the Rao quadratic entropy (and related indices). These indices are often regarded as redundant and promote the unsubstantiated yet widely held view that Rao is a form of MPD. Worryingly, existing R functions also do not always simplify the use and differentiation of these indices. In this paper, we show various distinctions between these two indices that warrant by showing an existing form of MPD that considers species abundances and is different from Rao both mathematically and conceptually. We then show that the mathematical relationship between MPD and Rao can be presented simply as Rao = MPD × Simpson, where the Simpson diversity index is defined as 1-dominance. We further show that this relationship is maintained for both species abundances and presence/absence. This evidence dismantles the paradigm that the Rao diversity is an abundance-weighted form of MPD and indicates that both indices can differ substantially at low species diversities. We discuss the different interpretations of trait diversity patterns in biological communities provided by Rao and MPD and then provide a simple R function, called “melodic,” which avoids the unintended results that arise from existing mainstream functions.},
-author = {de Bello, Francesco and Carmona, Carlos P. and Lep{\v{s}}, Jan and Szava-Kovats, Robert and P{\"{a}}rtel, Meelis},
-doi = {10.1007/s00442-016-3546-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Bello et al. - 2016 - Functional diversity through the mean trait dissimilarity resolving shortcomings with existing paradigms and al.pdf:pdf},
-journal = {Oecologia},
-number = {4},
-pages = {933--940},
-title = {{Functional diversity through the mean trait dissimilarity: resolving shortcomings with existing paradigms and algorithms}},
-url = {http://link.springer.com/10.1007/s00442-016-3546-0},
-volume = {180},
-year = {2016}
-}
-@article{Mason2013,
-abstract = {Question Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients? Methods We used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait-independent stochastic processes – mass and priority effects – in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of functional richness – total functional dendrogram length (FD) and convex hull volume (FRic) – with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence – Rao quadratic entropy (Rao) and functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. This converts them to pure measures of functional divergence (SESRao and SESFDis). Results When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness. Conclusions Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.},
-author = {Mason, Norman W. H. and de Bello, Francesco and Mouillot, David and Pavoine, Sandrine and Dray, St{\'{e}}phane},
-doi = {10.1111/jvs.12013},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mason et al. - 2013 - A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {794--806},
-title = {{A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients}},
-url = {http://doi.wiley.com/10.1111/jvs.12013},
-volume = {24},
-year = {2013}
-}
-@article{Chao2017,
-abstract = {1. Due to sampling limitations, almost every biodiversity survey misses species that are present, but not detected, so that empirical species counts underestimate species richness. A wide range of species richness estimators has been proposed in the literature to reduce undersampling bias. We focus on nonparametric estimators, which make no assumptions about themathematical formof the underlying species abundance/incidence distributions. 2. For replicated incidence data, in which only species presence/absence (or detection/non-detection) is recorded in multiple sampling units,most existing nonparametric estimators of the number of undetected species are based on the frequency counts of the uniques (species detected in only one sampling unit) and duplicates (species detected in exactly twosampling units). 3. Some survey methods, however, record only uniques and super-duplicates (species observed inmore than one sampling unit). Using the Good–Turing frequency formula, we developed a method to estimate the number of duplicates for such data, allowing estimation of true species richness, including undetected species. 4. We test our estimators on several empirical datasets for which doubletons were recorded and on simulated sampling data, then apply them to an extensive, but previously unusable survey of coral reef fishes, for which only uniques and super-duplicates were recorded. 5. We extend themethod to abundance data and discuss other potential applications.},
-author = {Chao, Anne and Colwell, Robert K. and Chiu, Chun-Huo and Townsend, Ditch},
-doi = {10.1111/2041-210X.12768},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2017 - Seen once or more than once applying Good-Turing theory to estimate species richness using only unique observations.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-title = {{Seen once or more than once: applying Good-Turing theory to estimate species richness using only unique observations and a species list}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12768},
-volume = {in press},
-year = {2017}
-}
-@article{Giller2004,
-abstract = {Recent experiments, mainly in terrestrial environments, have provided evidence of the functional importance of biodiversity to ecosystem processes and properties. Compared to terrestrial systems, aquatic ecosystems are characterised by greater propagule and material exchange, often steeper physical and chemical gradients, more rapid biological processes and, in marine systems, higher metazoan phylogenetic diversity. These characteristics limit the potential to transfer conclusions derived from terrestrial experiments to aquatic ecosystems whilst at the same time provide opportunities for testing the general validity of hypotheses about effects of biodiversity on ecosystem functioning. Here, we focus on a number of unique features of aquatic experimental systems, propose an expansion to the scope of diversity facets to be considered when assessing the functional consequences of changes in biodiversity and outline a hierarchical classification scheme of ecosystem functions and their corresponding response variables. We then briefly highlight some recent controversial and newly emerging issues relating to biodiversity-ecosystem functioning relationships. Based on lessons learnt from previous experimental and theoretical work, we finally present four novel experimental designs to address largely unresolved questions about biodiversity-ecosystem functioning relationships. These include (1) investigating the effects of non-random species loss through the manipulation of the order and magnitude of such loss using dilution experiments; (2) combining factorial manipulation of diversity in interconnected habitat patches to test the additivity of ecosystem functioning between habitats; (3) disentangling the impact of local processes from the effect of ecosystem openness via factorial manipulation of the rate of recruitment and biodiversity within patches and within an available propagule pool; and (4) addressing how non-random species extinction following sequential exposure to different stressors may affect ecosystem functioning. Implementing these kinds of experimental designs in a variety of systems will, we believe, shift the focus of investigations from a species richness-centred approach to a broader consideration of the multifarious aspects of biodiversity that may well be critical to understanding effects of biodiversity changes on overall ecosystem functioning and to identifying some of the potential underlying mechanisms involved.},
-author = {Giller, Paul S. and Hillebrand, Helmut and Berninger, Ulrike-G. and Gessner, Mark O. and Hawkins, Stephen and Inchausti, Pablo and Inglis, Cheryl and Leslie, Heather and Malmqvist, Bj{\"{o}}rn and Monaghan, Michael T. and Morin, Peter J. and O'Mullan, Gregory},
-doi = {10.1111/j.0030-1299.2004.13253.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Giller et al. - 2004 - Biodiversity effects on ecosystem functioning emerging issues and their experimental test in aquatic environments.pdf:pdf},
-journal = {Oikos},
-number = {3},
-pages = {423--436},
-title = {{Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0030-1299.2004.13253.x/abstract},
-volume = {104},
-year = {2004}
-}
-@article{Brulhart2005,
-abstract = {We use entropy indices to describe sectoral location patterns across Western European regions over the 1975–2000 period. Entropy measures are decomposable, and they lend themselves to statistical inference via associated bootstrap tests. We find that the geographic concentration of aggregate employment, as well as of most market services, has not changed statistically significantly over our sample period. Manufacturing, however, has become significantly more concentrated relative to the distribution of aggregate employment (increased “relative concentration”), while becoming significantly less concentrated relative to physical space (decreased “topographic concentration”). The contribution of manufacturing to the topographic concentration of aggregate employment has fallen from 26{\%} to 13{\%} over our sample period.},
-author = {Br{\"{u}}lhart, Marius and Traeger, Rolf},
-doi = {10.1016/j.regsciurbeco.2004.09.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Br{\"{u}}lhart, Traeger - 2005 - An Account of Geographic Concentration Patterns in Europe.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {6},
-pages = {597--624},
-title = {{An Account of Geographic Concentration Patterns in Europe}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046204000857},
-volume = {35},
-year = {2005}
-}
-@article{Myllymaki2013,
-abstract = {Envelope tests are a popular tool in spatial statistics, where they are used in goodness-of-fit testing. These tests graphically compare an empirical function T(r) with its simulated counterparts from the null model. However, the type I error probabil- ity $\alpha$ is conventionally controlled for a fixed distance r only, whereas the functions are inspected on an interval of distances I. In this study, we propose two approaches related to Barnard's Monte Carlo test for building global envelope tests on I: (1) ordering the empirical and simulated functions based on their r-wise ranks among each other, and (2) the construction of envelopes for a deviation test. These new tests allow the a priori selection of the global $\alpha$ and they yield p-values. We illustrate these tests using simulated and real point pattern data.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1307.0239v2},
-author = {Myllym{\"{a}}ki, Mari and Mrkvi{\v{c}}ka, Tom{\'{a}}{\v{s}} and Grabarnik, Pavel and Seijo, Henri and Hahn, Ute},
-eprint = {arXiv:1307.0239v2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Myllym{\"{a}}ki et al. - 2013 - Global envelope tests for spatial processes.pdf:pdf},
-journal = {arXiv},
-number = {v4},
-title = {{Global envelope tests for spatial processes}},
-url = {http://arxiv.org/abs/1307.0239},
-volume = {1307.0239},
-year = {2013}
-}
-@article{Kindt2006,
-abstract = {Species diversity is a function of the number of species and the evenness in the abundance of the component species. We calculated diversity and evenness profiles, which allowed comparing the diversity and evenness of communities. We applied the methodology to investigate differences in diversity among the main functions of trees on western Kenyan farms. Many use-groups (all trees and species that provide a specific use) could not be ranked in diversity or evenness. No use-group had perfectly even distributions. Evenness could especially be enhanced for construction materials, fruit, ornamental, firewood, timber and medicine, which included some of the most species-rich groups of the investigated landscape. When considering only the evenness in the distribution of the dominant species, timber, medicine, fruit and beverage ranked lowest ({\textgreater} 60{\%} of trees belonged to the dominant species of these groups). These are also use-groups that are mainly grown by farmers to provide cash through sales. Since not all communities can be ranked in diversity, studies that attempt to order communities in diversity should not base the ordering on a single index, or even a combination of several indices, but use techniques developed for diversity ordering such as the R{\'{e}}nyi diversity profile. The rarefaction of diversity profiles described in this article could be used in studies that compare results from surveys with different sample sizes. {\textcopyright} Springer 2006.},
-annote = {Cited By (since 1996): 12
-Export Date: 8 November 2012
-Source: Scopus
-CODEN: BONSE
-Language of Original Document: English
-Correspondence Address: Kindt, R.; ICRAF, PO Box 30677-00100, Nairobi, Kenya; email: R.Kindt@CGIAR.org},
-author = {Kindt, R. and {Van Damme}, P. and Simons, A. J.},
-doi = {10.1007/s10531-005-0772-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kindt, Van Damme, Simons - 2006 - Tree diversity in western Kenya Using profiles to characterise richness and evenness.pdf:pdf},
-journal = {Biodiversity and Conservation},
-number = {4},
-pages = {1253--1270},
-title = {{Tree diversity in western Kenya: Using profiles to characterise richness and evenness}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs10531-005-0772-x},
-volume = {15},
-year = {2006}
-}
-@article{Guan2008,
-abstract = {The paper introduces a new approach to estimate the variance of statistics that are computed from an inhomogeneous spatial point process. The approach proposed is based on the assumption that the observed point process can be thinned to be a second-order stationary point process, where the thinning probability depends only on the first-order intensity function of the (unthinned) original process. The resulting variance estimator is proved to be asymptotically consistent for the target parameter under some very mild conditions. The use of the approach proposed is demonstrated in two important applications of modelling inhomogeneous spatial point processes: residual diagnostics of a fitted model and inference on the unknown regression coefficients. A simulation study and an application to a real data example are used to demonstrate the efficacy of the approach proposed.},
-annote = {cited By (since 1996) 0},
-author = {Guan, Yontao},
-doi = {10.1111/j.1467-9868.2007.00632.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2008 - Variance estimation for statistics computed from inhomogeneous spatial point processes.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {175--190},
-title = {{Variance estimation for statistics computed from inhomogeneous spatial point processes}},
-volume = {70},
-year = {2008}
-}
-@article{Wright2005,
-abstract = {•Global-scale quantification of relationships between plant traits gives insight into the evolution of the world's vegetation, and is crucial for parameterizing vegetation–climate models. •A database was compiled, comprising data for hundreds to thousands of species for the core ‘leaf economics' traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. •While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation–climate models could incorporate this knowledge. •The core leaf traits were intercorrelated, both globally and within plant functional types, forming a ‘leaf economics spectrum'. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.},
-author = {Wright, Ian J. and Reich, Peter B. and Cornelissen, Johannes H. C. and Falster, Daniel S. and Garnier, Eric and Hikosaka, Kouki and Lamont, Byron B. and Lee, William and Oleksyn, Jacek and Osada, Noriyuki and Poorter, Hendrik and Villar, Rafael and Warton, David I. and Westoby, Mark},
-doi = {10.1111/j.1469-8137.2005.01349.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2005 - Assessing the generality of global leaf trait relationships.pdf:pdf},
-journal = {New Phytologist},
-number = {2},
-pages = {485--496},
-title = {{Assessing the generality of global leaf trait relationships}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2005.01349.x/abstract},
-volume = {166},
-year = {2005}
-}
-@unpublished{Ottaviano2003,
-abstract = {The purpose of the paper is to enrich the standard toolbox for measuring diversity in economics. In so doing, we compare the indicators of diversity used by economists with those used by biologists and ecologists. Ecologists and biologists are concerned about biodiversity: The diversity of organisms that inhabit a given area. Concepts of species diversity such as alpha (diversity within community), beta (diversity across communities) and gamma (diversity due to differences among samples when they are combined into a single sample) have been developed (Whittaker, 1960). Biodiversity is more complex than just the species that are present, it includes species richness and species evenness. Those various aspects of diversity are measured by biodiversity indices such as Simpson's Diversity Indices, Species Richness Index, Shannon Weaver Diversity Indices, Patil and Taillie Index, Modified Hill's Ratio. In economics, diversity measures are multi-faceted ranging from inequality (Lorenz curve, Gini coefficient, quintile distribution), to polarisation (Esteban and Ray, 1994; Wolfon, 1994, D'Ambrosio (2001)) and heterogeneity (Alesina, Baqir and Hoxby, 2000). We propose an interdisciplinary comparison between indicators. In particular, we review their theoretical background and applications. We provide an assessment of their possible use and interest according to their specific properties.},
-author = {Ottaviano, Gianmarco I. P. and Pinelli, Dino and Maignan, Carole Juliette and Rullani, Francesco},
-doi = {10.2139/ssrn.389043},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ottaviano et al. - 2003 - Bio-Ecological Diversity vs. Socio-Economic Diversity A Comparison of Existing Measures.pdf:pdf},
-series = {FEEM Working Paper},
-title = {{Bio-Ecological Diversity vs. Socio-Economic Diversity: A Comparison of Existing Measures}},
-url = {http://ssrn.com/abstract=389043},
-year = {2003}
-}
-@article{Calcagno2017,
-abstract = {Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.},
-author = {Calcagno, Vincent and Jarne, Philippe and Loreau, Michel and Mouquet, Nicolas and David, Patrice},
-doi = {10.1038/ncomms15810},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Calcagno et al. - 2017 - Diversity spurs diversification in ecological communities.pdf:pdf},
-issn = {2041-1723},
-journal = {Nature Communications},
-pages = {15810},
-title = {{Diversity spurs diversification in ecological communities}},
-url = {http://www.nature.com/doifinder/10.1038/ncomms15810},
-volume = {8},
-year = {2017}
-}
-@article{VandenHeuvel2014,
-abstract = {This article presents a method to identify "Absolute and Relative Employment Concentration (AREC) areas" for a particular industry. Two novel characteristics of the method are that it simultaneously analyses AREC, and that it combines spatial concentration per area with the spatial concentration in neighbouring areas. The method is easy to understand and apply. It is developed to assist regional policy makers and corporate decision-makers with their investment decisions related to new infrastructure or plants. The identification of concentration areas also allows for analysing the performance of these areas in relation to characteristics such as infrastructure availability and the housing and labour market. This can yield new academic insights that are relevant for regional planners. An application of the newly developed method to five industries in a Dutch province subdivided into 502 areas illustrates the value of the method in comparison to other methods. {\textcopyright} 2012 Taylor {\&} Francis.},
-annote = {Export Date: 30 January 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: van den Heuvel, F. P.; School of Industrial Engineering, Eindhoven University of Technology, PO Box 513, PAV F10, 5600 MB Eindhoven, Netherlands; email: f.p.v.d.heuvel@tue.nl
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(2003) Journal of Economic Geography, 3 (1), pp. 5-35; Maurel, F., Sedillot, B., A measure of the geographic concentration in French manufacturing industries (1999) Regional Science and Urban Economics, 29 (5), pp. 575-604; Moran, P.A.P., Notes on continuous stochastic phenomena (1950) Biometrika Trust, 37 (1-2), pp. 17-23; Mori, T., Nishikimi, K., Smith, T.E., A divergence statistic for industrial localization (2005) The Review of Economics and Statistics, 87 (4), pp. 635-651; Newlands, D., Competition and cooperation in industrial clusters: The implications for public policy (2003) European Planning Studies, 11 (5), pp. 521-532; O'Donoghue, D., Gleave, B., A note on methods for measuring industrial agglomeration (2004) Regional Studies, 38 (4), pp. 419-427; Porter, M.E., Clusters and the new economics of competition (1998) Harvard Business Review, pp. 77-90. , November-December; Porter, M.E., Location, competition, and economic development: Local clusters in a global economy (2000) Economic Development Quarterly, 14 (1), pp. 15-34; Pouder, R., St. John, C.H., Hot spots and blind spots: Geographical clusters of firms and innovation (1996) Academy of Management Review, 21 (4), pp. 1192-1225; Taniguchi, E., Noritake, M., Yamada, T., Izumitani, T., Optimal size and location planning of public logistics terminals (1999) Transportation Research Part E, 35 (3), pp. 207-222; Torre, A., Rallet, A., Proximity and localization (2005) Regional Studies, 39 (1), pp. 47-59; Van Soest, D.P., Gerking, S., Van Oort, F.G., Spatial impacts of agglomeration externalities (2006) Journal of Regional Science, 46 (5), pp. 881-899; Wennberg, K., Lindqvist, G., The effect of clusters on the survival and performance of new firms (2010) Small Business Economics, 34 (3), pp. 221-241},
-author = {van den Heuvel, F P and de Langen, P W and van Donselaar, K H and Fransoo, J C},
-doi = {10.1080/09654313.2012.741573},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/van den Heuvel et al. - 2014 - Identification of Employment Concentration Areas.pdf:pdf},
-journal = {European Planning Studies},
-number = {1},
-pages = {204--226},
-title = {{Identification of Employment Concentration Areas}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84891857548{\&}partnerID=40{\&}md5=d3c2ac67b03bfbe7aebc126ed8ccbece},
-volume = {22},
-year = {2014}
-}
-@article{Guitet2014,
-abstract = {Analyses of tree diversity and community composition in tropical rain forests are usually based either on general herbarium data or on a restricted number of botanical plots. Despite their high taxonomic accuracy, both types of data are difficult to extrapolate to landscape scales. Meanwhile, forestry surveys provide quantitative occurrence data on large areas, and are thus increasingly used for landscape-scale analyses of tree diversity. However, the reliability of these approaches has been challenged because of the ambiguity of the common (vernacular) names used by foresters and the complexity of tree taxonomy in those hyper-diverse communities.We developed and tested a novel approach to evaluate taxonomic reliability of forestry surveys and to propagate the resulting uncertainty in the estimates of several diversity indicators (alpha and beta entropy, Fisher-alpha and S{\{}{\o}{\}}rensen similarity). Our approach is based on Monte-Carlo processes that simulate communities by taking into account the expected accuracy and reliability of common names. We tested this method in French Guiana, on 9 one-hectare plots (4279 trees -- DBH. {\textgreater}=. 10. cm) for which both common names and standardized taxonomic determinations were available. We then applied our method of community simulation on large forestry inventories (560. ha) at the landscape scale and compared the diversity indices obtained for 10 sites with those computed from precise botanical determination situated at the same localities.We found that taxonomic reliability of forestry inventories varied from 22{\%} (species level) to 83{\%} (family level) in this Amazonian region. Indices computed directly with raw forestry data resulted in incorrect values, except for Gini-Simpson beta-diversity. On the contrary, our correction method provides more accurate diversity estimates, highly correlated with botanical measurements, for almost all diversity indices at both regional and local scales. We obtained a robust ranking of sites consistent with those shown by botanical inventories.These results show that (i) forestry inventories represent a significant part of taxonomic information, (ii) the relative diversity of regional sites can be successfully ranked using forestry inventory data using our method and (iii) forestry inventories can valuably contribute to the detection of large-scale diversity patterns when biases are well-controlled and corrected.The tools we developed as R-functions are available in supplementary material and can be adapted with local parameters to be used for forest management and conservation issues in other regional contexts. {\{}$\backslash$textcopyright{\}} 2014 Elsevier B.V.},
-author = {Guitet, St{\'{e}}phane and Sabatier, Daniel and Brunaux, Olivier and H{\'{e}}rault, Bruno and Aubry-Kientz, M{\'{e}}laine and Molino, Jean-Fran{\c{c}}ois and Baraloto, Christopher},
-doi = {10.1016/j.foreco.2014.05.045},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guitet et al. - 2014 - Estimating tropical tree diversity indices from forestry surveys A method to integrate taxonomic uncertainty.pdf:pdf},
-journal = {Forest Ecology and Management},
-pages = {270--281},
-title = {{Estimating tropical tree diversity indices from forestry surveys: A method to integrate taxonomic uncertainty}},
-url = {http://www.sciencedirect.com/science/article/pii/S037811271400351X},
-volume = {328},
-year = {2014}
-}
-@article{Ricotta2017,
-abstract = {The amount of variation in species composition among sampling units or beta diversity has become a primary tool for connecting the spatial structure of species assemblages to ecological processes. Many different measures of beta diversity have been developed. Among them, the total variance in the community composition matrix has been proposed as a single-number estimate of beta diversity. In this study, I first show that this measure summarizes the compositional variation among sampling units after nonlinear transformation of species abundances. Therefore, it is not always adequate for estimating beta diversity. Next, I propose an alternative approach for calculating beta diversity in which variance is substituted by a weighted measure of concentration (i.e., an inverse measure of evenness). The relationship between this new measure of beta diversity and so-called multiple-site dissimilarity measures is also discussed.},
-author = {Ricotta, Carlo},
-doi = {10.1002/ece3.2980},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2017 - Of beta diversity, variance, evenness, and dissimilarity.pdf:pdf},
-issn = {20457758},
-journal = {Ecology and Evolution},
-number = {13},
-pages = {4835--4843},
-title = {{Of beta diversity, variance, evenness, and dissimilarity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.2980/full},
-volume = {7},
-year = {2017}
-}
-@incollection{Bierlaire1998,
-abstract = {Discrete choice models have played an important role in transportation modeling for the last 25 years. They are namely used to provide a detailed representation of the complex aspects of transportation demand, based on strong theoretical justifications. Moreover, several packages and tools are available to help practionners using these models for real applications, making discrete choice models more and more popular. Discrete choice models are powerful but complex. The art of finding the appropriate model for a particular application requires from the analyst both a close familiarity with the reality under interest and a strong understanding of the methodological and theoretical background of the model. The main theoretical aspects of discrete choice models are reviewed in this paper. The main assumptions used to derive discrete choice models in general, and random utility models in particular, are covered in detail. The Multinomial Logit Model, the Nested Logit Model and the Generalized Extreme Value model are also discussed.},
-author = {Bierlaire, Michel},
-booktitle = {Operations Research and Decision Aid Methodologies in Traffic and Transportation Management},
-editor = {Labb{\'{e}}, M and Laporte, G and Tanczos, K and Toint, Ph.},
-pages = {203--227},
-publisher = {Springer},
-title = {{Discrete choice models}},
-url = {http://rosowww.epfl.ch/mbi/papers/discretechoice/paper.html},
-year = {1998}
-}
-@article{Janzen1970a,
-abstract = {Wet lowland tropical forests characteristically have many tree species and low density of adults of each species compared with temperate-zone forests in habitats of similar areal extent, topographic diversity, and edaphic complexity (Black, Dobzhansky, and Pavan 1950 ; Richards 1952 ; Poore 1968; Ashton 1969). Despite reports that adults of some species of lowland tropical trees show clumped distributions (Poore 1968; Ashton 1969), I believe that a third generalization is possible about tropical tree species as contrasted with temperate ones: for most species of lowland tropical trees, adults do not produce new adults in their immediate vicinity (where most seeds fall). Because of this, most adults of a given tree species appear to be more regularly distributed than if the probability of a new adult appearing at a point in the forest were proportional to the number of seeds arriving at that point. This generalization is based on my observa- tions in Central and South American mainland forests, on discussions with foresters familiar with these forests, on discussions with J. H. Connell about Australian rain forests, and on data given in the papers cited above.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Janzen, Daniel H.},
-doi = {10.1086/282687},
-eprint = {arXiv:1011.1669v3},
-isbn = {1630130044},
-issn = {0003-0147},
-journal = {The American Naturalist},
-number = {940},
-pages = {501--528},
-pmid = {17891731},
-title = {{Herbivores and the Number of Tree Species in Tropical Forests}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/282687},
-volume = {104},
-year = {1970}
-}
-@article{Swenson2011,
-abstract = {Explaining the mechanisms that produce the enormous diversity within and between tropical tree communities is a pressing challenge for plant community ecologists. Mechanistic hypotheses range from niche-based deterministic to dispersal-based stochastic models. Strong tests of these hypotheses require detailed information regarding the functional strategies of species. A few tropical studies to date have examined trait dispersion within individual forest plots using species trait means in order to ask whether coexisting species tend to be more or less functionally similar than expected given a null model. The present work takes an alternative approach by: (i) explicitly incorporating population-level trait variability; and (ii) quantifying the functional beta diversity in a series of 15 tropical forest plots arrayed along an elevational gradient. The results show a strong pattern of decay in community functional similarity with elevation. These observed patterns of functional beta diversity are shown to be highly non-random and support a deterministic model of tropical tree community assembly and turnover.},
-author = {Swenson, Nathan G. and Anglada-Cordero, Pedro and Barone, John A.},
-doi = {10.1098/rspb.2010.1369},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Swenson, Anglada-Cordero, Barone - 2011 - Deterministic tropical tree community turnover evidence from patterns of functional beta.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {1707},
-pages = {877--884},
-title = {{Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient}},
-url = {http://rspb.royalsocietypublishing.org/content/278/1707/877.article-info},
-volume = {278},
-year = {2011}
-}
-@article{Nazareno2017,
-abstract = {Introduction: D-dimer assay, generally evaluated according to cutoff points calibrated for VTE exclusion, is used to estimate the individual risk of recurrence after a first idiopathic event of venous thromboembolism (VTE). Methods: Commercial D-dimer assays, evaluated according to predetermined cutoff levels for each assay, specific for age (lower in subjects {\textless}70 years) and gender (lower in males), were used in the recent DULCIS study. The present analysis compared the results obtained in the DULCIS with those that might have been had using the following different cutoff criteria: traditional cutoff for VTE exclusion, higher levels in subjects aged ≥60 years, or age multiplied by 10. Results: In young subjects, the DULCIS low cutoff levels resulted in half the recurrent events that would have occurred using the other criteria. In elderly patients, the DULCIS results were similar to those calculated for the two age-adjusted criteria. The adoption of traditional VTE exclusion criteria would have led to positive results in the large majority of elderly subjects, without a significant reduction in the rate of recurrent event. Conclusion: The results confirm the usefulness of the cutoff levels used in DULCIS.},
-author = {Nazareno, Alison G. and Dick, Christopher W. and Lohmann, L{\'{u}}cia G.},
-doi = {10.1111/mec.14142},
-isbn = {4955139574},
-issn = {1365294X},
-journal = {Molecular Ecology},
-number = {14},
-pages = {3636--3648},
-pmid = {28199780},
-title = {{Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species}},
-volume = {26},
-year = {2017}
-}
-@article{Caylor2003a,
-abstract = {Spatial pattern in tree distribution is examined at 10 sites along the IGBP Kalahari Transect in southern Africa in order to examine the patterns of community structure across a large average annual rainfall gradient. Analysis indicates aggregation among all individuals in the vegetation communities at most sites; with-no occurrence of aggregation in individuals at the most southern arid site: The spatial distribution for the largest 25{\%} of individuals is predominantly random. Uniform pattern is only observed in the distribution, of canopy dominants at one site. A comparison between expected and observed densities of understory vegetation beneath large trees shows significant patterns at six of ten sites, with lower than expected values at both the northern and southernmost sites in the transect, and significantly higher than expected values at intermediate sites. Variation in the spatial distribution of understory individuals with respect to - larger canopy individuals suggests that distribution of suitable regeneration sites and. subsequent patterns of establishment may be critical phenomena in determining the spatial pattern of vegetation.},
-annote = {Article
-English
-J ARID ENVIRON
-671ZL},
-author = {Caylor, K. K. and Shugart, H. H. and Dowty, P. R. and Smith, T. M.},
-doi = {10.1006/jare.2002.1090},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Caylor et al. - 2003 - Tree spacing along the Kalahari transect in southern Africa.pdf:pdf},
-journal = {Journal of Arid Environments},
-number = {2},
-pages = {281--296},
-title = {{Tree spacing along the Kalahari transect in southern Africa}},
-url = {http://www.sciencedirect.com/science/article/pii/S0140196302910906},
-volume = {54},
-year = {2003}
-}
-@article{Clench1979,
-abstract = {Procedures are described for making two types of regional lists of butterflies: the state or provincial list, and the "local study" (an intensive, long-term investigation of a small area). The need for such lists, problems in making them, and some of the expectable results, are examined. A logarithmic scale for describing pop- ulation sizes is given, as is a procedure for estimating total number of species in a local area.},
-author = {Clench, Harry K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clench - 1979 - How to make regional lists of butterflies some thoughts.pdf:pdf},
-journal = {Journal of the Lepidopterists' Society},
-number = {4},
-pages = {216--231},
-title = {{How to make regional lists of butterflies: some thoughts}},
-volume = {33},
-year = {1979}
-}
-@article{Ord1995,
-abstract = {The statistics Gi(d) and Gi*(d), introduced in Getis and Ord (1992) for the study of local pattern in spatial data, are extended and their properties further explored. In particular, nonbinary weights are allowed and the statistics are related to Moran's autocorrelation statistic, I. The correlations between nearby values of the statistics are derived and verified by simulation. A Bonferroni criterion is used to approximate significance levels when testing extreme values from the set of statistics. An example of the use of the statistics is given using spatial-temporal data on the AIDS epidemic centering on San Francisco. Results indicate that in recent years the disease is intensifying in the counties surrounding the city.},
-annote = {Logiciel sur http://www.uottawa.ca/academic/arts/geographie/lpcweb/newlook/data{\_}and{\_}downloads/download/sawsoft/gistats.htm},
-author = {Ord, J. K. and Getis, Arthur},
-doi = {10.1111/j.1538-4632.1995.tb00912.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ord, Getis - 1995 - Local spatial autocorrelation statistics distributional issues and an application.pdf:pdf},
-journal = {Geographical Analysis},
-number = {4},
-pages = {286--296},
-title = {{Local spatial autocorrelation statistics: distributional issues and an application}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1995.tb00912.x/abstract},
-volume = {27},
-year = {1995}
-}
-@article{Presley2014,
-abstract = {Growing interest in understanding ecological patterns from phylogenetic and functional perspectives has driven the development of metrics that capture variation in evolutionary histories or ecological functions of species. Recently, an integrated framework based on Hill numbers was developed that measures three dimensions of biodiversity based on abundance, phylogeny and function of species. This framework is highly flexible, allowing comparison of those diversity dimensions, including different aspects of a single dimension and their integration into a single measure. The behavior of those metrics with regard to variation in data structure has not been explored in detail, yet is critical for ensuring an appropriate match between the concept and its measurement. We evaluated how each metric responds to particular data structures and developed a new metric for functional biodiversity. The phylogenetic metric is sensitive to variation in the topology of phylogenetic trees, including variation in the relative lengths of basal, internal and terminal branches. In contrast, the functional metric exhibited multiple shortcomings: (1) species that are functionally redundant contribute nothing to functional diversity and (2) a single highly distinct species causes functional diversity to approach the minimum possible value. We introduced an alternative, improved metric based on functional dispersion that solves both of these problems. In addition, the new metric exhibited more desirable behavior when based on multiple traits.},
-author = {Presley, Steven J. and Scheiner, Samuel M. and Willig, Michael R.},
-doi = {10.1371/journal.pone.0105818},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Presley, Scheiner, Willig - 2014 - Evaluation of an integrated framework for biodiversity with a new metric for functional dispersion.pdf:pdf},
-journal = {PloS one},
-number = {8},
-pages = {e105818},
-title = {{Evaluation of an integrated framework for biodiversity with a new metric for functional dispersion.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4141827{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {9},
-year = {2014}
-}
-@article{Gregorius2015,
-abstract = {Biological variation is commonlymeasured at two basic levels: variation within individual communities, and the distribution of variation over communities or within ametacommunity. We develop a classification for the measurement of biological variation on both levels: With- in communities into the categories of dispersion and diversity, and within metacommunities into the categories of compositional differentiation and partitioning of variation. There are essentially two approaches to characterizing the distribution of trait variation over communi- ties in that individuals with the same trait state or type tend to occur in the same community (describes differentiation tendencies), and individuals with different types tend to occur in different communities (describes apportionment tendencies). Both approaches can be viewed from the dual perspectives of trait variation distributed over communities (CT per- spective) and community membership distributed over trait states (TC perspective). This classification covers most of the relevant descriptors (qualified measures) of biological vari- ation, as is demonstrated with the help of major families of descriptors. Moreover, the classi- fication is shown to open ways to develop new descriptors that meet current needs. Yet the classification also reveals the misclassification of some prominent and widely applied de- scriptors: Dispersion is oftenmisclassified as diversity, particularly in cases where disper- sion descriptor allow for the computation of effective numbers; the descriptorGST of population genetics is commonly misclassified as compositional differentiation and con- fused with partitioning-oriented differentiation, whereas it actually measures partitioning- oriented apportionment; descriptors of $\beta$-diversity are ambiguous about the differentiation effects they are supposed to represent and therefore require conceptual reconsideration. Introduction},
-author = {Gregorius, Hans-Rolf and Gillet, Elizabeth M.},
-doi = {10.1371/journal.pone.0115312},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius, Gillet - 2015 - Classifying Measures of Biological Variation.pdf:pdf},
-journal = {Plos One},
-number = {3},
-pages = {e0115312},
-title = {{Classifying Measures of Biological Variation}},
-url = {http://dx.plos.org/10.1371/journal.pone.0115312},
-volume = {10},
-year = {2015}
-}
-@article{Peterson1999,
-abstract = {The relationship between photosynthetic carbon assimilation (Amax) and leaf nitrogen content (Nleaf) can be expressed on either a leaf area basis (Aarea vs Narea) or a leaf mass basis (Amass vs Nmass). Dimensional analysis shows that the units for the slope of this relationship are the same for both expressions (mol [CO2] g-1 [N] s-1). Thus the slope measures the change in CO2 assimilation per gram of nitrogen, independent of leaf mass or leaf area. Although they have the same units, large di.erences between the area and mass-based slopes have been observed over a broad range of taxonomically diverse species. Some authors have claimed that regardless of these differences, the fundamental nature of the Amax-Nleaf relationship is independent of the units of expression. In contrast, other authors have claimed that the area-based Amax-Nleaf relationship is fundamentally di.erent from the mass-based relationship because of interactions between Amax, Nleaf, and leaf mass per area (LMA, g [leaf] m)2 [leaf]). In this study we consider the mathematical relationships involved in the transformation from mass- to area-based expressions (and vice versa), and the implications this transformation has for the slope of the Amax-Nleaf relationship. We then show that the slope of the relationship is independent of the units of expression when the e.ect of LMA is controlled statistically using a multiple regression. The validity of this hypothesis is demonstrated using 13 taxonomically and functionally diverse C3 species. This analysis shows that the slope of the Amax-Nleaf relationship is similar for the mass- and area-based expressions and that significant errors in the estimate of the slope can arise when the effect of LMA is not controlled.},
-author = {Peterson, Andrew G and CMEAL participants},
-doi = {10.1007/s004420050712},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peterson, CMEAL participants - 1999 - Reconciling the apparent difference between mass- and area-based expressions of the photosynthesis.pdf:pdf},
-journal = {Oecologia},
-pages = {114--150},
-title = {{Reconciling the apparent difference between mass- and area-based expressions of the photosynthesis-nitrogen relationship.}},
-volume = {118},
-year = {1999}
-}
-@article{Lawton1988,
-abstract = {The patterns and processes of canopy tree death and replacement were studied in the elfin forest of Monteverde, Costa Rica. Natural treefalls and limbfalls in a 5.2-ha study area opened 0.8, 1.4, and 1.0{\%} of the area in three consecutive years with about four gaps/ha/yr larger than 4 m2. Forty-one percent of the gaps were formed by uprooted trees, 39{\%} by snapped trees, and the remainder by limbfall, the collapse of epiphyte masses, and dead standing trees killed by lightning. Gaps were found to be spatially aggregated, with more gaps occurring within 17-20 m of one another than expected by chance. Variation among gaps was complex; the first principal component of the variation in eight important gap characteristics among 88 gaps contrasted measures of gap size with the way the gapmaker broke and the position of the gap on the slope, but accounted for only 56{\%} of the total variation. In gaps {\textless} 8 mo old, the leaf area index was 1.6, and only 8{\%} of the area was not covered by living plants. Leaf area index increased logarithmically with time since gap formation and with gap area; 50{\%} of the mature-forest leaf area index of 5.1 was recovered in 3 yr in gaps of 10 m2 and in 1.5 yr in gaps of 40 m2. Saplings of both shade-tolerant and shade-intolerant canopy tree species were more abundant in gaps than in the understory of mature forest. Sapling density increased with time since gap formation, but, given the effect of time, shade-tolerant sapling density decreased with gap area, while shade-intolerant sapling density increased. Saplings of eight species were concentrated on nurse logs, while those of one other species were concentrated on the mineral soil disturbed by uprooting trees. Experimental investigation of colonization of exposed soil in treefall gaps indicated that buried seeds give rise to many more tree seedlings than seeds dispersed into recent gaps. Many of the saplings in gaps, however, started life as epiphytic seedlings in the crowns of the trees that fell. The dynamics of this lower montane rain forest resemble many lowland forests in regards to the importance of gap-phase regeneration but differ in the sources of canopy gap colonists and in the importance of different substrates for seedling establishment.},
-author = {Lawton, Robert O. and Putz, Francis E.},
-doi = {10.2307/1941025},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lawton, Putz - 1988 - Natural Disturbance and Gap-Phase Regeneration in a Wind-Exposed Tropical Cloud Forest.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {764--777},
-title = {{Natural Disturbance and Gap-Phase Regeneration in a Wind-Exposed Tropical Cloud Forest}},
-url = {https://www.jstor.org/stable/1941025},
-volume = {69},
-year = {1988}
-}
-@article{Jackle2017,
-abstract = {The Tsallis entropy given for a positive parameter {\$}\backslashalpha{\$} can be considered as a modification of the classical Shannon entropy. For the latter, corresponding to {\$}\backslashalpha=1{\$}, there exist many axiomatic characterizations. One of them based on the well-known Khinchin-Shannon axioms has been simplified several times and adapted to Tsallis entropy, where the axiom of (generalized) Shannon additivity is playing a central role. The main aim of this paper is to discuss this axiom in the context of Tsallis entropy. We show that it is sufficient for characterizing Tsallis entropy with the exceptions of cases {\$}\backslashalpha=1,2{\$} discussed separately.},
-archivePrefix = {arXiv},
-arxivId = {1704.08011},
-author = {J{\"{a}}ckle, Sonja and Keller, Karsten},
-eprint = {1704.08011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/J{\"{a}}ckle, Keller - 2017 - Tsallis entropy and generalized Shannon additivity.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Tsallis entropy and generalized Shannon additivity}},
-url = {http://arxiv.org/abs/1704.08011},
-volume = {1704.08011},
-year = {2017}
-}
-@article{Helmus2007,
-abstract = {We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid-tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith's phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy-to-understand package of phylogenetic measures of species variability, richness, and evenness with well-defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.},
-author = {Helmus, Matthew R. and Bland, Thomas J. and Williams, Christopher K. and Ives, Anthony R.},
-doi = {10.1086/511334},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Helmus et al. - 2007 - Phylogenetic measures of biodiversity.pdf:pdf},
-journal = {The American naturalist},
-number = {3},
-pages = {E68--83},
-title = {{Phylogenetic measures of biodiversity}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/17230400},
-volume = {169},
-year = {2007}
-}
-@article{Condit2000,
-abstract = {Fully mapped tree census plots of large area, 25 to 52 hectares, have now been completed at six different sites in tropical forests, including dry deciduous to wet evergreen forest on two continents. One of the main goals of these plots has been to evaluate spatial patterns in tropical tree populations. Here the degree of aggregation in the distribution of 1768 tree species is examined based on the average density of conspecific trees in circular neighborhoods around each tree. When all individuals larger than 1 centimeter in stem diameter were included, nearly every species was more aggregated than a random distribution. Considering only larger trees ({\textgreater}= 10 centimeters in diameter), the pattern persisted, with most species being more aggregated than random. Rare species were more aggregated than common species. All six forests were very similar in all the particulars of these results. The},
-author = {Condit, Richard and Ashton, Peter S. and Baker, Patrick and Bunyavejchewin, Sarayudh and Gunatilleke, Savithri and Gunatilleke, Nimal and Hubbell, Stephen P. and Foster, Robin B. and Itoh, Akira and LaFrankie, James V. and Lee, Hua Seng and Losos, Elizabeth and Manokaran, N. and Sukumar, Raman and Yamakura, Takuo},
-doi = {10.1126/science.288.5470.1414},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Condit et al. - 2000 - Spatial Patterns in the Distribution of Tropical Tree Species.pdf:pdf},
-journal = {Science},
-number = {5470},
-pages = {1414--1418},
-title = {{Spatial Patterns in the Distribution of Tropical Tree Species}},
-url = {http://www.sciencemag.org/cgi/content/abstract/288/5470/1414},
-volume = {288},
-year = {2000}
-}
-@article{Kelly2002,
-abstract = {Sudden Oak Death is caused by a newly discovered virulent pathogen (Phytophthora ramorum) that is killing thousands of native oak (Quercus) trees in California, USA. We present a landscape-scale study on the spatio-temporal dynamics of oak mortality. Second-order spatial point-pattern analysis techniques (Ripley's K) were applied to the distribution of dead tree crowns (derived from high-resolution imagery) in Marin County, California to determine the existence and scale of mortality clustering in two years (2000 and 2001). Both years showed clustering patterns between 100 and 300 m. A classification tree model was developed to predict spatial patterns of risk for oak mortality based on several landscape-scale variables. Proximity to forest edge was the most important explanatory factor, followed by topographic moisture index, proximity to trails, abundance of Umbellularia californica, and potential summer solar radiation. This research demonstrates the utility of integrating remotely sensed imagery analysis with geographic information systems and spatial modelling for understanding the dynamics of exotic species invasions.},
-author = {Kelly, Maggi and Meentemeyer, Ross K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kelly, Meentemeyer - 2002 - Landscape dynamics of the spread of Sudden Oak Death.pdf:pdf},
-journal = {PE{\&}RS, Photogrammetric Engineering {\&} Remote Sensing},
-number = {10},
-pages = {1001--1009},
-title = {{Landscape dynamics of the spread of Sudden Oak Death}},
-volume = {68},
-year = {2002}
-}
-@misc{Hubbell2005,
-author = {Hubbell, Stephen P. and Condit, Richard and Foster, Robin B.},
-title = {{Barro Colorado Forest Census Plot Data}},
-url = {https://ctfs.arnarb.harvard.edu/webatlas/datasets/bci.},
-year = {2005}
-}
-@article{Halpern1995,
-abstract = {With the exception of the tropics, nowhere has the relationship between resource management and conservation of biological diversity been more controversial than in the Pacific Northwest region of the United States. Widespread loss and fragmentation of old-growth ecosystems have stimulated critical review and revision of existing forest management policies. However, studies of the consequences of forest management for plant species diversity are sorely lacking. We present data from permanent-plot and chronose- quence studies in managed and unmanaged forests of western Oregon and Washington to describe the early responses of understory communities to forest harvest, and to suggest how post-harvest practices that alter natural successional processes may influence long- term patterns of diversity and species occurrence. Permanent-plot studies of early succession in old-growth Pseudotsuga forests suggest that changes in understory diversity are fairly short-lived following clear-cut logging and slash burning. Populations of most vascular plant species recover to original levels prior to canopy closure. However, diversity may remain depressed for more than two decades on severely burned sites, and some species may experience local extinction. Evidence of the effects of post-harvest practices on vascular plant diversity is limited by an absence of community-level studies in older, managed forests. Chronosequence studies of natural forest stands indicate that, following canopy closure, vascular plant species diversity tends to increase with time, peaking in old growth. Few understory species are restricted to, or absent from, any stage of stand development (i.e., young, mature, or old growth). However, many species differ significantly in their abundance among stages. A majority of these showed greatest abundance in old growth. Changes in levels of resources (increased shade), changes in the spatial variability of resources and environments (increased horizontal and vertical heterogeneity), and species' sensitivity to fire and slow rates of reestablishment/growth may drive these trends during natural stand development. Silvicultural prescriptions that maintain or foster spatial and temporal diversity of re- sources and environments will be most effective in maintaining plant species diversity. Practices associated with intensive, short-rotation plantation forestry, that preclude or delay the development of old-growth attributes, may result in long-term loss of diversity. Ulti- mately, it may be necessary to manage some stands on long rotations (150-300 yr) to maintain understory species that require long periods to recover from disturbance.},
-author = {Halpern, Charles B. and Spies, Thomas A.},
-doi = {10.2307/2269343},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Halpern, Spies - 1995 - Plant species diversity in natural and managed forests of the Pacific Northwest.pdf:pdf},
-journal = {Ecological Applications},
-number = {4},
-pages = {913--934},
-title = {{Plant species diversity in natural and managed forests of the Pacific Northwest}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/2269343/full},
-volume = {5},
-year = {1995}
-}
-@article{Ricotta2016a,
-abstract = {The preservation of ecosystem processes under ongoing biotic erosion requires that some species within affected communities perform similar functions, a property that is usually defined as functional redundancy. Although functional redundancy has recently become a relevant part of ecological research, so far there is no agreement on its measurement. The scope of this work is thus to propose a consistent framework based on functional dissimilarities among species for summarizing different facets of functional redundancy. The behaviour of the proposed measures is illustrated with one small artificial data set, together with actual examples on the species functional turnover along successional gradients. We believe this new framework provides an important contribution for the clarification and quantification of key metrics of community redundancy and vulnerability. The method, for which we provide a simple r function called ‘uniqueness', further allows summarizing the functional contribution of single species to the overall redundancy of any type of biological community.},
-author = {Ricotta, Carlo and de Bello, Francesco and Moretti, Marco and Caccianiga, Marco and Cerabolini, Bruno E. L. and Pavoine, Sandrine},
-doi = {10.1111/2041-210X.12604},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2016 - Measuring the functional redundancy of biological communities a quantitative guide.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {11},
-pages = {1386--1395},
-title = {{Measuring the functional redundancy of biological communities: a quantitative guide}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12604/full},
-volume = {7},
-year = {2016}
-}
-@article{Naudts2002,
-abstract = {Criteria are given that kappa-deformed logarithmic and exponential functions should satisfy. With a pair of such functions one can associate another function, called the deduced logarithmic function. It is shown that generalized thermostatistics can be formulated in terms of kappa-deformed exponential functions together with the associated deduced logarithmic functions. (C) 2002 Elsevier Science B.V. All rights reserved.},
-annote = {Naudts, J},
-author = {Naudts, Jan},
-doi = {10.1016/s0378-4371(02)01018-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Naudts - 2002 - Deformed exponentials and logarithms in generalized thermostatistics.pdf:pdf},
-isbn = {0378-4371},
-journal = {Physica A},
-number = {1-4},
-pages = {323--334},
-title = {{Deformed exponentials and logarithms in generalized thermostatistics}},
-volume = {316},
-year = {2002}
-}
-@article{Veech2010,
-author = {Veech, Joseph A. and Crist, Thomas O.},
-doi = {doi:10.1890/09-1140.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veech, Crist - 2010 - Toward a unified view of diversity partitioning.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1988--1992},
-title = {{Toward a unified view of diversity partitioning}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-1140.1},
-volume = {91},
-year = {2010}
-}
-@book{Cabrera-Gaillard1990,
-address = {Kourou},
-author = {Cabrera-Gaillard, Claudio and Gignoux, Jacques},
-pages = {1--42},
-publisher = {Centre Technique de la For{\^{e}}t Tropicale},
-title = {{R{\'{e}}partition spatiale et sylviculture en for{\^{e}}t guyanaise}},
-year = {1990}
-}
-@article{Sweeney1998,
-abstract = {Although a growing number of studies emphasize the advantages small firms gain by co-locating in space, there is little empirical work that directly examines clustering trends by firm size. This paper presents an empirical analysis of the isolated effects of size on clustering patterns of producers in a major manufacturing state in the southeast United States. Recent developments in point process modeling allow us to control for the critical fact that economic activity is, in general, concentrated in space. Our findings suggest that the relationship between establishment size and clustering in North Carolina is roughly characterized by an inverted u-shape, that is, clustering increases up to some size threshold and then decreases again.},
-author = {Sweeney, Stuart H. and Feser, Edward J.},
-doi = {10.1111/j.1538-4632.1998.tb00388.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sweeney, Feser - 1998 - Plant Size and Clustering of Manufacturing Activity.pdf:pdf},
-journal = {Geographical Analysis},
-number = {1},
-pages = {45--64},
-title = {{Plant Size and Clustering of Manufacturing Activity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1998.tb00388.x/abstract},
-volume = {30},
-year = {1998}
-}
-@article{VanderPlas2016,
-abstract = {Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystemfunctions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species ($\alpha$-diversity) and their turnover between plots ($\beta$-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between $\alpha$-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between $\beta$-diversity and landscape-scale multifunctionality were always positive, because a high spatial turn- over in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.},
-author = {van der Plas, Fons and Manning, Peter and Soliveres, Santiago and Allan, Eric and Scherer-Lorenzen, Michael and Verheyen, Kris and Wirth, Christian and Zavala, Miguel A. and Ampoorter, Evy and Baeten, Lander and Barbaro, Luc and Bauhus, J{\"{u}}rgen and Benavides, Raquel and Benneter, Adam and Bonal, Damien and Bouriaud, Olivier and Bruelheide, Helge and Bussotti, Filippo and Carnol, Monique and Castagneyrol, Bastien and Charbonnier, Yohan and Coomes, David Anthony and Coppi, Andrea and Bestias, Cristina C. and Dawud, Seid Muhie and {De Wandeler}, Hans and Domisch, Timo and Fin{\'{e}}r, Leena and Gessler, Arthur and Granier, Andr{\'{e}} and Grossiord, Charlotte and Guyot, Virginie and H{\"{a}}ttenschwiler, Stephan and Jactel, Herv{\'{e}} and Jaroszewicz, Bogdan and Joly, Fran{\c{c}}ois-xavier and Jucker, Tommaso and Koricheva, Julia and Milligan, Harriet and Mueller, Sandra and Muys, Bart and Nguyen, Diem and Pollastrini, Martina and Ratcliffe, Sophia and Raulund-Rasmussen, Karsten and Selvi, Federico and Stenlid, Jan and Valladares, Fernando and Vesterdal, Lars and Ziel{\'{i}}nski, Dawid and Fischer, Markus},
-doi = {10.1073/pnas.1517903113},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/van der Plas et al. - 2016 - Biotic homogenization can decrease landscape-scale forest multifunctionality.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {13},
-pages = {3557--3562},
-title = {{Biotic homogenization can decrease landscape-scale forest multifunctionality}},
-url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1517903113},
-volume = {113},
-year = {2016}
-}
-@article{Dale2001a,
-abstract = {This paper describes new methods for the detection of the characteristics of spatial point patterns. based on counting plants in the circumcircles of triangles defined by triplets of the points themselves. In addition to counting points in the circumcircle, a further refinement is to count also the points in a ring around the circumcircle of the same area. This approach can be applied in a univariate form, with one species or one kind of plant, to detect and evaluate the best-defined patches of plants and gaps. In the bivariate form. the method can be used to investigate the spatial characteristics of the relationship between different kinds of plants. These methods are illustrated by application to several data sets. In particular, the method is shown to be useful in describing the spatial relationship between seedlings and trees, both when the seedlings are on the forest floor beneath the canopy trees and when the seedlings represent post-fire regeneration.},
-annote = {Article
-English
-J VEG SCI
-503DV},
-author = {Dale, Mark R. T. and Powell, R. D.},
-doi = {10.2307/3236899},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dale, Powell - 2001 - A new method for characterizing point patterns in plant ecology.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {597--608},
-title = {{A new method for characterizing point patterns in plant ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236899/abstract},
-volume = {12},
-year = {2001}
-}
-@article{MacArthur1965,
-abstract = {1. Species diversity is most simply measured by counting species. More complicated measures, which take into account the relative abundance of the species, have been derived from information theory or from parameters of statistical distributions fitted to the census data. The information theory formulae can also be used to measure habitat diversity and differences between communities or habitats. In this way, changes in the pattern of species diversity can be compared with changes in the environment. 2. Small or remote islands and islands with uniform topography have fewer species than large or complex islands or islands nearer the source of colonization. For birds and some orders of insects it appears that the rate of colonization of new species is virtually balanced by the rate of extinction, so that the number of species has reached equilibrium. For other organisms, such as mammals, and for all organisms on the most remote islands, this equilibrium has probably not been reached and further increases in the fauna may be expected. The comparison of impoverished island faunas with the mainland faunas whence they were derived shows the effect of relaxed competition. 3. Local variations in the species diversity of small uniform habitats can usually be predicted in terms of the structure and productivity of the habitat. Habitats of similar structure on islands and mainland often have similar species diversities; the impoverishment of the island is reflected in the fact that different habitats on the island have nearly the same species, while different habitats on the mainland have more different species. This is interpreted as evidence that uniform habitats are nearly saturated with species and that new species usually colonize by occupying different habitats from present species. 4. The theory of competition and the facts of character displacement indicate that there is a limiting similarity to species which co-exist within a habitat. Species more similar than this limiting value must occupy different habitats. According to the theory, this limiting value should be less where productivity is high, where family size is low and where the seasons are relatively uniform. It should also be less for pursuing hunters than for species which search for stationary prey. 5. Total species diversities, from areas composed of many types of habitat, are usually, but not always, much greater in the tropics than in temperate regions. This is accomplished by a finer subdivision of habitats (habitat selection) more than by a marked increase in diversity within habitats. This total diversity may still be increasing and may have not reached saturation.},
-annote = {10.1111/j.1469-185X.1965.tb00815.x},
-author = {MacArthur, Robert H.},
-doi = {10.1111/j.1469-185X.1965.tb00815.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacArthur - 1965 - Patterns of species diversity.pdf:pdf},
-journal = {Biological Reviews},
-number = {4},
-pages = {510--533},
-title = {{Patterns of species diversity}},
-url = {http://dx.doi.org/10.1111/j.1469-185X.1965.tb00815.x},
-volume = {40},
-year = {1965}
-}
-@article{Ricotta2005e,
-abstract = {Ecologists have long recognized three different components of species diversity: alpha or within-community diversity ($\alpha$), beta or between-community diversity ($\beta$) and gamma or total species diversity in a region ($\gamma$). In this framework, $\beta$-diversity has been traditionally linked to the other diversity components through a multiplicative model so that it can be expressed as the ratio between $\gamma$-diversity and average $\alpha$-diversity in a set of plots. Yet, more recently, ecologists are starting to partition diversity using the lesser known approach that $\alpha$- and $\beta$-diversities sum to give the $\gamma$-diversity. This additive diversity partitioning is based on the decomposition of concave diversity measures for which the total diversity in a pooled set of communities exceeds (or equals) the average diversity within communities. In this paper, first, I shortly revise additive diversity partitioning for traditional diversity measures that are computed from species relative abundances. Next, I show that, under some specific circumstances, the same model can be extended to Rao's quadratic entropy, a measure that combines species relative abundances and pairwise interspecies differences. Finally, in the framework of taxonomic diversity, Rao's quadratic entropy has another decomposition: the sum over the Simpson indices at all the taxonomic levels. Thus, I show that, combining both partitioning models, the contribution of each level in the taxonomic hierarchy to the $\alpha$- $\beta$- and $\gamma$-diversity components of Rao's quadratic entropy is made explicit. The proposed diversity decomposition is illustrated with a worked example on data from a plant community on ultramafic soils in Tuscany (central Italy).},
-author = {Ricotta, Carlo},
-doi = {http://dx.doi.org/10.1016/j.ecolmodel.2004.08.020},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2005 - Additive partitioning of Rao's quadratic diversity a hierarchical approach.pdf:pdf},
-journal = {Ecological Modelling},
-number = {4},
-pages = {365--371},
-title = {{Additive partitioning of Rao's quadratic diversity: a hierarchical approach}},
-url = {http://www.sciencedirect.com/science/article/pii/S030438000400496X},
-volume = {183},
-year = {2005}
-}
-@article{Wiegand1999,
-abstract = {We construct and explore a general modeling framework that allows for a systematic investigation of the impact of changes in landscape structure on population dynamics. The essential parts of the framework are a landscape generator with independent control over landscape composition and physiognomy, an individual‐based spatially explicit population model that simulates population dynamics within heterogeneous landscapes, and scale‐dependent landscape indices that depict the essential aspects of landscape that interact with dispersal and demographic processes. Landscape maps are represented by a grid of cells and consist of good‐quality, poor‐quality, or uninhabitable matrix habitat cells. The population model was shaped in accordance to the biology of European brown bears (Ursus arctos), and demographic parameters were adjusted to yield a source‐sink configuration. Results obtained with the spatially explicit model do not confirm results of earlier nonspatial source‐sink models where addition of sink habitat resulted in a decrease of total population size because of dilution of high‐quality habitat. Our landscape indices, which describe scale‐dependent correlation between and within habitat types, were able to explain variations in variables of population dynamics (mean number of females with sink home ranges, mean number of females with source home ranges, and mean dispersal distance) caused by different landscape structure. When landscape structure changed, changes in these variables generally followed the corresponding change of an appropriate landscape index in a linear way. Our general approach incorporates source‐sink dynamics as well as metapopulation dynamics, and the population model can easily be modified for other species groups.},
-author = {Wiegand, Thorsten and Moloney, Kirk A. and Naves, Javier and Knauer, Felix},
-doi = {10.1086/303272},
-journal = {The American Naturalist},
-number = {6},
-pages = {605--627},
-title = {{Finding the Missing Link between Landscape Structure and Population Dynamics: A Spatially Explicit Perspective}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/303272},
-volume = {154},
-year = {1999}
-}
-@article{Head1999,
-abstract = {We study Japanese investments between 1980 and 1992 to assess the effectiveness of US state promotion efforts in light of strong agglomeration effects in Japanese investment. The provision of foreign trade zones, lower taxes, and job-creation subsidies have statistically significant effects on the location of investment. Simulations indicate that unilateral withdrawal of promotion would have caused individual states to lose substantial amounts of Japanese investment. However, because state promotional policies tended to offset each other, their impact on the geographic distribution of Japanese investment appears small.},
-author = {Head, Keith and Ries, John and Swenson, Deborah},
-doi = {10.1016/S0166-0462(98)00029-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Head, Ries, Swenson - 1999 - Attracting Foreign Manufacturing Investment Promotion and Agglomeration.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {2},
-pages = {197--218},
-title = {{Attracting Foreign Manufacturing: Investment Promotion and Agglomeration}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046298000295},
-volume = {29},
-year = {1999}
-}
-@article{Banavar2010,
-abstract = {There are numerous situations in physics and other disciplines which can be described at different levels of detail in terms of probability distributions. Such descriptions arise either intrinsically as in quantum mechanics, or because of the vast amount of details necessary for a complete description as, for example, in Brownian motion and in many-body systems. We show that an application of the principle of maximum entropy for estimating the underlying probability distribution can depend on the variables used for describing the system. The choice of characterization of the system carries with it implicit assumptions about fundamental attributes such as whether the system is classical or quantum mechanical or equivalently whether the individuals are distinguishable or indistinguishable. We show that the correct procedure entails the maximization of the relative entropy subject to known constraints and, additionally, requires knowledge of the behavior of the system in the absence of these constraints. We present an application of the principle of maximum entropy to understanding species diversity in ecology and introduce a new statistical ensemble corresponding to the distribution of a variable population of individuals into a set of species not defined a priori.},
-author = {Banavar, Jayanth R. and Maritan, Amos and Volkov, Igor},
-doi = {10.1088/0953-8984/22/6/063101},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Banavar, Maritan, Volkov - 2010 - Applications of the principle of maximum entropy from physics to ecology.pdf:pdf},
-isbn = {0953-8984$\backslash$r1361-648X},
-issn = {0953-8984},
-journal = {Journal of Physics: Condensed Matter},
-number = {6},
-pages = {063101},
-title = {{Applications of the principle of maximum entropy: from physics to ecology}},
-url = {http://stacks.iop.org/0953-8984/22/i=6/a=063101?key=crossref.55e86d0921c6ab5a0a05105dc42579ca},
-volume = {22},
-year = {2010}
-}
-@article{Mcintosh1967,
-author = {Mcintosh, Robert P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mcintosh - 1967 - An Index of Diversity and the Relation of Certain Concepts to Diversity.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {392--404},
-title = {{An Index of Diversity and the Relation of Certain Concepts to Diversity}},
-volume = {48},
-year = {1967}
-}
-@article{Redding2010,
-abstract = {Although a rich and extensive body of theoretical research on new economic geography has emerged, empirical research remains comparatively less well developed. This paper reviews the existing empirical literature on the predictions of new economic geography models for the distribution of income and production across space. The discussion highlights connections with other research in regional and urban economics, identification issues, potential alternative explanations, and possible areas for further research.},
-author = {Redding, Stephen J.},
-doi = {10.1111/j.1467-9787.2009.00646.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Redding - 2010 - The Empirics of New Economic Geography.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {1},
-pages = {297--311},
-title = {{The Empirics of New Economic Geography}},
-volume = {50},
-year = {2010}
-}
-@article{Lloyd1964,
-abstract = {We recognize two distinct components of species diversity: the number of species and the `equitability' with which the individuals are apportioned among the species. A quantitative expression for `equitability' per se is derived from the Shannon-Wiener function, using MacArthur's `broken-stick' model as a yardstick, and a table is provided which greatly reduces the necessary calculations. The appropriate use of this formula, and the sampling problems, depend very much on whether one is trying to describe the local conditions of association under which the animals are living or whether one is interested in characterizing the fauna of a large area as a whole.},
-annote = {ArticleType: research-article / Full publication date: Jun., 1964 / Copyright {\^{A}}{\textcopyright} 1964 British Ecological Society},
-author = {Lloyd, Monte and Ghelardi, R J},
-doi = {10.2307/2628},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lloyd, Ghelardi - 1964 - A Table for Calculating the 'Equitability' Component of Species Diversity.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {2},
-pages = {217--225},
-title = {{A Table for Calculating the 'Equitability' Component of Species Diversity}},
-url = {http://www.jstor.org/stable/2628},
-volume = {33},
-year = {1964}
-}
-@article{StuartChapin1990,
-author = {Chapin, F. Stuart III and Schulze, Ernst-Detlef and Mooney, Harold A.},
-doi = {10.1146/annurev.es.21.110190.002231},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chapin, Schulze, Mooney - 1990 - The Ecology and Economics of Storage in Plants.pdf:pdf},
-journal = {Annual Review of Ecology and Systematics},
-pages = {423--447},
-title = {{The Ecology and Economics of Storage in Plants}},
-url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.es.21.110190.002231},
-volume = {21},
-year = {1990}
-}
-@article{Lisingo2015,
-abstract = {L'{\'{e}}valuation de la diversit{\'{e}} sp{\'{e}}cifique demeure un outil indispensable dans la mise en place des strat{\'{e}}gies de conservation de la biodiversit{\'{e}} et d'am{\'{e}}nagement des {\'{e}}cosyst{\`{e}}mes. En for{\^{e}}t tropicale humide, la richesse et la diversit{\'{e}} sp{\'{e}}cifique sont presque toujours {\'{e}}lev{\'{e}}es mais varient dans l'espace. Plusieurs {\'{e}}tudes ont {\'{e}}t{\'{e}} men{\'{e}}es {\`{a}} l'{\'{e}}chelle locale pour {\'{e}}valuer la richesse et la composition floristique des for{\^{e}}ts de la cuvette centrale congolaise. Gr{\^{a}}ce {\`{a}} une centaine des parcelles d'un inventaire que nous avons r{\'{e}}alis{\'{e}} dans quatre stations foresti{\`{e}}res au nord-est du bassin congolais, nous montrons que les peuplements d'arbres pr{\'{e}}sentent des variations notables dans leur diversit{\'{e}} sp{\'{e}}cifique et leur composition floristique. Les sites septentrionaux de l'Ituri et de Rubi-Tele sont localement moins diversifi{\'{e}}s que ceux de Yoko et Uma aux environs de Kisangani.},
-author = {Lisingo, Janvier and Dauby, Gilles and Hardy, Olivier J. and Boyemba, Faustin and Makana, Jean-R{\'{e}}my and Ndjele, L{\'{e}}opold},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lisingo et al. - 2015 - Structures spatiales de la richesse sp{\'{e}}cifique dans quelques blocs forestiers du nord-est du bassin congolais i.pdf:pdf},
-journal = {Geo-Eco-Trop},
-number = {2},
-pages = {169--184},
-title = {{Structures spatiales de la richesse sp{\'{e}}cifique dans quelques blocs forestiers du nord-est du bassin congolais : implication pour la diversit{\'{e}} r{\'{e}}gionale et la conservation}},
-url = {http://www.geoecotrop.be/index.php?page=numero-39},
-volume = {39},
-year = {2015}
-}
-@incollection{Gove1994,
-abstract = {The diversity of an ecological community isdefined in terms of the average species rarity ofthat community using both dichotomous- and rank- type rarily measures. Common diversity indices and profiles are developed using thisdefinition and theconcept ofintrinsic diversity orderingispresented. The use of these diversity measures is illustrated in casestudies involving the plant communities in twodistinct forested ecosystems ofthe southeastern and northeastern United Slates. In these case studies, the objective is the compara tiveassessment of diversity changes over lime and between treatments. Diver sity profiles are further utilized in nonlinear mathematical programming models for uneven-aged stand management. The models present strategies for maximization and maintenance of structural diversity within uneven-aged stands. Finally, a principal components regression technique is presented which facilitates prediction of plant species diversity; theuser need onlybeable to classify an individual intooneoflive life-forms significantly reducing the taxonomic skills required for diversity assessment.},
-author = {Gore, Jeffrey H. and Patil, Ganapati P. and Swindel, Benee F. and Taillie, Charles},
-booktitle = {Handbook of Statistics, vol.12},
-doi = {10.1016/S0169-7161(05)80014-8},
-editor = {Rao, C. Radhakrishna and Patil, Ganapati P.},
-pages = {409--462},
-publisher = {Elsevier},
-title = {{Ecological Diversity and Forest Management}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169716105800148},
-volume = {12},
-year = {1994}
-}
-@article{Bartik1985,
-abstract = {This article examines how corporate decisions about the location for a new manufacturing plant in the U.S. are influenced by unionization, taxes, and other characteristics of states. The conditional logit model is used with some modifications to make the model more applicable to the business location decision. The most important finding is that the union sympathies of states have a major effect on business location. The results also indicate that state taxes affect business location, contradicting the conventional wisdom in the economic literature, although the tax effect is of modest magnitude.},
-author = {Bartik, Timothy J.},
-doi = {10.2307/1391685},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bartik - 1985 - Business Location Decisions in the United States Estimates of the Effects of Unionization, Taxes, and Other Characterist.pdf:pdf},
-journal = {Journal of Business and Economic Statistics},
-number = {1},
-pages = {14--22},
-title = {{Business Location Decisions in the United States: Estimates of the Effects of Unionization, Taxes, and Other Characteristics of States}},
-url = {https://www.jstor.org/stable/1391685},
-volume = {3},
-year = {1985}
-}
-@article{Mouillot2005a,
-abstract = {Functional diversity has been identified as a key to understanding ecosystem and community functioning. However, due to the lack of a sound definition its nature and measurement are still poorly understood. In the same way that species diversity can be split into species richness and species evenness, so functional diversity can be split into functional richness (i.e. the amount of functional trait/character/attribute space filled) and functional evenness (i.e. the evenness of abundance distribution in functional trait space). We propose a functional regularity index (FRO) as a measure of functional evenness for situations where species are represented only by a single functional trait value (e.g. mean, median or mode), and species abundances are known. This new index is based on the Bulla O index of species evenness. When dealing with functional types or categorical functional traits, the Bulla O or any other accepted species evenness index may be used directly to measure functional evenness. The advantage of FRO is that it supplies a measure of functional evenness for continuous trait data. The FRO index presented in this paper fulfils all the a priori criteria required. We demonstrate with two example datasets that a range of FRO values may be obtained for both plant and animal communities. Moreover, FRO was strongly related to ecosystem function as seen in photosynthetic biomass in plant communities, and was able to differentiate sampling stations in a lagoon based on the functional traits of fish. Thus, the FRO index is potentially a highly useful tool for measuring functional diversity in a variety of ecological situations.},
-author = {Mouillot, David and Mason, W. H. Norman and Dumay, Olivier and Wilson, J. Bastow},
-doi = {10.1007/s00442-004-1744-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouillot et al. - 2005 - Functional regularity a neglected aspect of functional diversity.pdf:pdf},
-journal = {Oecologia},
-number = {3},
-pages = {353--359},
-title = {{Functional regularity: a neglected aspect of functional diversity}},
-volume = {142},
-year = {2005}
-}
-@article{Podani2006,
-abstract = {Euclidean distance is commonly involved in calculating functional diversity (FD), for example, in measures based on dendrogram branch lengths. We point out that this function is inappropriate in many cases and that the choice of clustering method is more crucial than earlier thought. Gower's formula and UPGMA clustering are suggested here as a standard combination of techniques for calculating FD. The advantage of Gower's measure is its suitability to a mixture of scale types and its tolerance to missing values. Examples demonstrate that UPGMA clustering is more robust and has a better goodness of fit to dissimilarities than complete and single linkage classifications. In addition, we propose that the effect of individual species on FD is best evaluated by species removals and subsequent comparisons of tree length values. The influence of each functional trait is optimally judged by considering both dendrogram length and topological changes.},
-author = {Podani, J{\'{a}}nos and Schmera, D{\'{e}}nes},
-doi = {10.1111/j.2006.0030-1299.15048.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani, Schmera - 2006 - On dendrogram-based measures of functional diversity.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {179--185},
-title = {{On dendrogram-based measures of functional diversity}},
-url = {http://dx.doi.org/10.1111/j.2006.0030-1299.15048.x},
-volume = {115},
-year = {2006}
-}
-@article{Ricklefs2014,
-abstract = {The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, ‘An equilibrium theory of insular zoogeography', was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re-assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution – understanding ecosystem functioning, speciation and diversification – frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future.},
-author = {Ricklefs, Robert E.},
-doi = {10.1111/ele.12398},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricklefs - 2014 - Islands as model systems in ecology and evolution prospects fifty years after MacArthur-Wilson.pdf:pdf},
-journal = {Ecology letters},
-number = {2},
-pages = {200--217},
-title = {{Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12398/abstract},
-volume = {18},
-year = {2015}
-}
-@incollection{Miller1955,
-author = {Miller, G. A.},
-booktitle = {Information Theory in Psychology: Problems and Methods},
-editor = {Quastler, Henry},
-pages = {95--100},
-publisher = {Free Press},
-title = {{Note on the bias of information estimates}},
-year = {1955}
-}
-@article{Grenie2017,
-abstract = {{\textcopyright} 2017 John Wiley {\&} Sons Ltd. Emphasis has been put in recent ecological research on investigating phylogenetic, functional and taxonomic facets of biological diversity. While a flourishing number of indices have been proposed for assessing functional diversity, surprisingly few options are available to characterize functional rarity. Functional rarity can play a key role in community and ecosystem dynamics. We introduce here the funrar R package to quantify functional rarity based on species trait differences and species frequencies at local and regional scales. Because of the increasing availability of big datasets in macroecology and biogeography, we optimized funrar to work with large datasets of thousands of species and sites. We illustrate the use of the package to investigate the functional rarity of North and Central American mammals.},
-author = {Greni{\'{e}}, Matthias and Denelle, Pierre and Tucker, Caroline M. and Munoz, Fran{\c{c}}ois and Violle, Cyrille},
-doi = {10.1111/ddi.12629},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Greni{\'{e}} et al. - 2017 - funrar An R package to characterize functional rarity.pdf:pdf},
-journal = {Diversity and Distributions},
-pages = {1365--1371},
-title = {{funrar: An R package to characterize functional rarity}},
-year = {2017}
-}
-@article{Billings2012a,
-abstract = {We introduce a non-parametric microdata based test for industrial specialization and apply it to a single urban area. Our test employs establishment densities for specific industries, a population counterfactual, and a new correction for multiple hypothesis testing to determine the statistical significance of special- ization across both places and industries. Results highlight patterns of specialization that are extremely varied, with downtown places specializing in a number of service sector industries, while suburban places specialize in both manufacturing and service industries. Business service industries are subject to more specialization than non-business service industries while the manufacturing sector contains the lowest representation of industries with specialized places. Finally, we compare results for specializa- tion with localization and show that both measures contribute to our understanding of industry and place specific agglomerative forces.},
-author = {Billings, Stephen B. and Johnson, Erik B.},
-doi = {10.1016/j.jue.2011.12.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Billings, Johnson - 2012 - A non-parametric test for industrial specialization.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {3},
-pages = {312--331},
-title = {{A non-parametric test for industrial specialization}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0094119011000805},
-volume = {71},
-year = {2012}
-}
-@article{Koh2012,
-abstract = {This paper assesses the agglomeration pattern of four-digit industries in Germany using a rich data set on the population of German firms. To identify geographical agglomeration, the distance-based approach of Duranton and Overman of 2005 is followed. It is found that the location pattern of 71{\%} of the manufacturing industries departs from randomness in the sense that plants exhibit significant geographical localization. In line with previous studies for the United Kingdom and France, the analysis suggests that especially traditional manufacturing industries exhibit strong localization patterns. Moreover, it is found that geographical localization is not restricted to the manufacturing sector, but that it plays an equally important role for service industries.},
-author = {Koh, Hyun-Ju and Riedel, Nadine},
-doi = {10.1080/00343404.2012.677024},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Koh, Riedel - 2012 - Assessing the Localization Pattern of German Manufacturing and Service Industries A Distance-based Approach.pdf:pdf},
-journal = {Regional Studies},
-number = {5},
-pages = {823--843},
-publisher = {Routledge},
-title = {{Assessing the Localization Pattern of German Manufacturing and Service Industries: A Distance-based Approach}},
-url = {http://dx.doi.org/10.1080/00343404.2012.677024},
-volume = {48},
-year = {2012}
-}
-@article{Ricotta2015b,
-abstract = {Multiple-site dissimilarity may be caused by two opposite processes of meta-community organization, such as species nestedness and turnover. Therefore, discriminating among these contributions is necessary for linking multiple-site dissimilarity to ecosystem functioning. This paper introduces a measure of multiple-site dissimilarity or beta diversity for presence/absence data that is based on information on species absences from the species × sites matrix. It is also shown that the newly proposed dissimilarity index can be additively partitioned into species nestedness and turnover.},
-author = {Ricotta, Carlo and Pavoine, Sandrine},
-doi = {10.1016/j.ecolind.2015.02.026},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Pavoine - 2015 - A multiple-site dissimilarity measure for species presenceabsence data and its relationship with nestedness an.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {203--206},
-title = {{A multiple-site dissimilarity measure for species presence/absence data and its relationship with nestedness and turnover}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X1500103X},
-volume = {54},
-year = {2015}
-}
-@article{Cadotte2015,
-abstract = {Species traits influence where species live and how they interact. While there have been many advances in describing the functional composition and diversity of communities, only recently do researchers have the ability to predict community composition and diversity. This predictive ability can offer fundamental insights into ecosystem resilience and restoration.},
-author = {Cadotte, Marc W. and Arnillas, Carlos A. and Livingstone, Stuart W. and Yasui, Simone Louise E.},
-doi = {10.1016/j.tree.2015.07.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte et al. - 2015 - Predicting communities from functional traits.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {9},
-pages = {510--511},
-title = {{Predicting communities from functional traits}},
-url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(15)00168-8},
-volume = {30},
-year = {2015}
-}
-@article{Auer2015,
-abstract = {Industries necessarily differ with respect to their type of geographical concentration. When some industries are overrepresented in urban areas (urban concentration), then some other industries must be overrepresented in rural areas (rural concentration). Unfortunately, the existing measures of concentration cannot distinguish between urban and rural concentration. They simply ignore the problem and rank industries with respect to their degree of concentration, even though these industries may exhibit completely different types of concentration. In the present paper we develop a new approach that avoids such misleading comparisons. Our approach distinguishes not only between urban and rural concentration but between seven different geographical patterns. The statistical identification of each industry's geographical pattern is based on two Goodman-Kruskal rank correlation coefficients and their bivariate confidence region. Using German employment data on 613 different industries, the power of our approach is demonstrated.},
-author = {von Auer, Ludwig and Stepayan, Andranik and Trede, Mark},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Auer, Stepayan, Trede - 2015 - Regional Concentration and Confidence Regions.pdf:pdf},
-journal = {ERSA conference papers},
-number = {564},
-pages = {1--24},
-title = {{Regional Concentration and Confidence Regions}},
-url = {https://ideas.repec.org/p/wiw/wiwrsa/ersa15p564.html},
-volume = {15},
-year = {2015}
-}
-@article{Møller2007,
-abstract = {We summarize and discuss the current state of spatial point process theory and directions for future research, making an analogy with generalized linear models and random effect models, and illustrating the theory with various examples of applications. In particular, we consider Poisson, Gibbs and Cox process models, diagnostic tools and model checking, Markov chain Monte Carlo algorithms, computational methods for likelihood-based inference, and quick non-likelihood approaches to inference.},
-author = {M{\o}ller, Jesper and Waagepetersen, Rasmus P.},
-doi = {10.1111/j.1467-9469.2007.00569.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/M{\o}ller, Waagepetersen - 2007 - Modern Statistics for Spatial Point Processes.pdf:pdf},
-journal = {Scandinavian Journal of Statistics},
-number = {4},
-pages = {643--684},
-title = {{Modern Statistics for Spatial Point Processes}},
-volume = {34},
-year = {2007}
-}
-@article{Vinck2012,
-abstract = {Estimating entropy from empirical samples of finite size is of central importance for information theory as well as the analysis of complex statistical systems. Yet, this delicate task is marred by intrinsic statistical bias. Here we decompose the entropy function into a polynomial approximation function and a remainder function. The approximation function is based on a Taylor expansion of the logarithm. Given n observations, we give an unbiased, linear estimate of the first n power series terms based on counting sets of k coincidences. For the remainder function we use nonlinear Bayesian estimation with a nearly flat prior distribution on the entropy that was developed by Nemenman, Shafee, and Bialek. Our simulations show that the combined entropy estimator has reduced bias in comparison to other available estimators.},
-annote = {ISI Document Delivery No.: 948VB
-Times Cited: 0
-Cited Reference Count: 30
-Vinck, Martin Battaglia, Francesco P. Balakirsky, Vladimir B. Vinck, A. J. Han Pennartz, Cyriel M. A.
-Vici[918.46.609]; eu[fp7-217148, fp7-ict-270108]
-We thank Dr. P. Gori-Giorgi for helpful comments on the manuscript. This work was supported by VICI Grant 918.46.609 and EU Grants FP7-217148 and FP7-ICT-270108.
-Amer physical soc
-College pk
-Part 1},
-author = {Vinck, Martin and Battaglia, Francesco P. and Balakirsky, Vladimir B. and Vinck, A. J. Han and Pennartz, Cyriel M. A.},
-doi = {10.1103/PhysRevE.85.051139},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vinck et al. - 2012 - Estimation of the entropy based on its polynomial representation.pdf:pdf},
-journal = {Physical Review E},
-number = {5},
-title = {{Estimation of the entropy based on its polynomial representation}},
-volume = {85},
-year = {2012}
-}
-@article{Whittaker1972,
-abstract = {Given a resource gradient (e.g. light intensity, prey size) in a community, species evolve to use different parts of this gradient; competition between them is thereby reduced. Species relationships in the community may be conceived in terms of a multidimensional coordinate system, the axes of which are the various resource gradients (and other aspects of species relationships to space, time, and one another in the community). This coordinate system defines a hyperspace, and the range of the space that a given species occupies is its niche hypervolume, as an abstract characterization of its intra-community position, or niche. Species evolve toward difference in niche, and consequently toward difference in location of their hypervolumes in the niche hyperspace. Through evolutionary time additional species can fit into the community in niche hypervolumes different from those of other species, and the niche hyperspace can become increasingly complex. Its complexity relates to the community's richness in species, its alpha diversity. Species differ in the proportions of the niche hyperspace they are able to occupy and the share of the community's resources they utilize. The share of resources utilized is expressed in species' productivities, and when species are ranked by relative productivity (or some other measurement) from most to least important, importance-value or dominance-diversity curves are formed. Three types of curves may represent manners in which resources are divided among species: (a) niche pre-emption with strong dominance, expressed in a geometric series, (b) random boundaries between niches, expressed in the MacArthur distribution, and (c) determination of relative importance by many factors, so that species form a frequency distribution on a logarithmic base of importance values, a lognormal distribution. The forms of importance-value curves do not permit strong inference about resource division, but are of interest for their expression of species relationships and bearing on measurement of diversity. Two aspects of alpha diversity are to be measured. Diversity in the strict sense is richness in species, and is appropriately measured as the number of species in a sample of standard size. Slope measurements, in contrast, express the steepness of the importance-value sequence. Of the slope measurements the Simpson index expresses dominance or relative concentration of the importance values into the first or first few species, whereas the Shannon-Wiener index expresses the relative evenness or equitability of the importance values through the whole sequence. A new index, expressing equitability as number of species per logarithmic cycle of the importance-value sequence, is suggested. Given a habitat gradient (e.g. elevation or soil moisture conditions) species evolve to occupy different positions along this gradient. The various habitat gradients of a landscape may also be conceived as a multidimensional hyperspace, and species evolve toward occupation of different positions in this hyperspace. Along a particular habitat gradient species populations have scattered centers and usually overlap broadly, forming a community continuum or coenocline. Through evolutionary time additional species can fit themselves in along the coenocline. As they do so the extent of change in community composition along the gradient increases. The extent of differentiation of communities along habitat gradients is beta diversity. The total or gamma diversity of a landscape, or geographic area, is a product of the alpha diversity of its communities and the degree of beta differentiation among them. The species' position in a landscape of communities, as described in terms of both habitat and niche relationships, may be termed its ecotope. Two approaches to measuring beta diversity have been most useful. For a transect along a given coenocline, the degree of species turnover or compositional change may be measured through sample similarities and expressed as half-changes. When a set of samples are taken to represent differences in communities of a landscape or range of habitat along more than one habitat axis, beta differentiation for these samples may be expressed by the ratio of the total number of species represented in the samples to the mean number per sample. Diversity of communities seems a resultant of non-extreme conditions, stable conditions, evolutionary and successional time, and the kind of community developed in that time. It is difficult to separate the effects of chronic environmental rigor, amplitude of regular fluctuation, and irregularity or unpredictableness of fluctuation. Diversities are low in many unstable environments, but certain desert communities subject to wide and irregular variation in precipitation have evolved high diversities in relation to this variation. Evolutionary time is difficult to measure, but is important as the dimension through which increase in alpha and beta diversity occurs. Alpha diversities of birds, and gamma diverstities of islands, appear to reach saturation or steady-state levels. It is suggested, however, that for terrestrial plants and insects increase of species diversity, with elaboration of the niche hyperspace and division of the habitat hyperspace, is a self-augmenting evolutionary process without any evident limit.},
-author = {Whittaker, R. H.},
-doi = {10.2307/1218190},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker - 1972 - Evolution and Measurement of Species Diversity.pdf:pdf},
-journal = {Taxon},
-number = {2/3},
-pages = {213--251},
-title = {{Evolution and Measurement of Species Diversity}},
-url = {http://www.jstor.org/stable/1218190},
-volume = {21},
-year = {1972}
-}
-@article{Baccini1988,
-abstract = {Dans cet article, on {\'{e}}tablit que les indices de concentration les plus souvent utilis{\'{e}}s, lorsque l'on {\'{e}}tudie l'in{\'{e}}galit{\'{e}} des revenus, du patrimoine..., peuvent {\^{e}}tre obtenus {\`{a}} partir de mesures classiques de dissemblance entre lois de probabilit{\'{e}}s. On obtient ainsi une pr{\'{e}}sentation simple et unifi{\'{e}}e de ces indices.},
-author = {Baccini, Alain and de Falguerolles, Antoine and Qannari, El Mostafa},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baccini, Falguerolles, Qannari - 1988 - Etude de quelques indices de concentration un essai de pr{\'{e}}sentation unifi{\'{e}}e.pdf:pdf},
-journal = {Revue de Statistique Appliqu{\'{e}}e},
-number = {1},
-pages = {31--44},
-title = {{Etude de quelques indices de concentration : un essai de pr{\'{e}}sentation unifi{\'{e}}e}},
-url = {http://www.numdam.org/item/RSA{\_}1986{\_}{\_}34{\_}1{\_}31{\_}0},
-volume = {34},
-year = {1988}
-}
-@incollection{Rosenthal2004,
-address = {Amsterdam},
-author = {Rosenthal, Stuart S. and Strange, William C.},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rosenthal, Strange - 2004 - Evidence on the Nature and Sources of Agglomeration Economics.pdf:pdf},
-publisher = {Elsevier. North Holland},
-title = {{Evidence on the Nature and Sources of Agglomeration Economics}},
-url = {http://www.hec.unil.ch/deep/evenements/3c-combes1.pdf},
-year = {2004}
-}
-@article{Garzon-Lopez2014,
-abstract = {Questions Niche differentiation is a central explanation for the co-existence and distribution patterns of numerous tree species in tropical forests, but functional equivalence leading to neutral dynamics has been proposed as an alternative explanation. This niche vs neutral debate is fuelled by the highly variable results yielded by studies of the association between tree species distributions and environmental factors, where some studies find strong associations but others do not. Here, we ask how differences in sampling scale between studies contribute to this variation. Location Barro Colorado Island, Panama. Methods Using distribution maps of canopy-statured individuals, we evaluated patterns of habitat association in five tropical tree species on Barro Colorado Island across a wide range of sampling scales (from 50 to 1600 ha). We investigated the scale-dependency of species clumping patterns (Ripley's K) and the association of species distributions with important environmental variables (forest age, topography and geological formation) using point pattern analyses. Results Clump size and clump density had high variances within and among spatial scales. Significant habitat associations were found in all five species, with the number of habitat associations generally increasing with the sampling scale. Ignoring dispersal constraints inflated the number of significant habitat associations. Conclusions We found that patterns of habitat association (and hence conclusions on the importance of niche vs neutral processes) are strongly affected by the choice of sampling scale and location. Explicit inclusion of the effect of spatial scale is critical for studies of habitat association and the main processes that structure communities of tropical trees.},
-author = {Garzon-Lopez, Carol X. and Jansen, Patrick A. and Bohlman, Stephanie A. and Ordonez, Alejandro and Olff, Han},
-doi = {10.1111/jvs.12090},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garzon-Lopez et al. - 2014 - Effects of sampling scale on patterns of habitat association in tropical trees.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {349--362},
-title = {{Effects of sampling scale on patterns of habitat association in tropical trees}},
-url = {http://doi.wiley.com/10.1111/jvs.12090},
-volume = {25},
-year = {2014}
-}
-@article{Wilson2012,
-abstract = {Questions The co-existence of high numbers of species has always fascinated ecologists, but what and where are the communities with the world records for plant species richness? The species–area relationship is among the best-known patterns in community ecology, but does it give a consistent global pattern for the most saturated communities, the global maxima? Location The world. Methods We assembled the maximum values recorded for vascular plant species richness for contiguous areas from 1 mm2 up to 1 ha. We applied the power function to relate maximal richness to area and to make extrapolations to the whole Earth. Results Only two community types contain global plant species maxima. The maxima at smaller spatial grain were from oligo- to meso-trophic, managed, semi-natural, temperate grasslands (e.g. 89 species on 1 m2), those at larger grains were from tropical rain forests (e.g. 942 species on 1 ha). The maximum richness values closely followed a power function with z = 0.250: close to Preston's ‘canonical' value of 0.262. There was no discernable difference between maxima using rooted presence (i.e. including only plants rooted in the plot) vs shoot presence (i.e. including any plant with physical cover over the plot). However, shoot presence values must logically be greater, with the curves flattening out at very small grain, and there is evidence of this from point quadrats. Extrapolating the curve to the terrestrial surface of the Earth gave a prediction of 219 204 vascular plant species, surprisingly close to a recent estimate of 275 000 actual species. Conclusions Very high richness at any spatial grain is found only in two particular habitat/community types. Nevertheless, these high richness values form a very strong, consistent pattern, not greatly affected by the method of sampling, and this pattern extrapolates amazingly well. The records challenge ecologists to consider mechanisms of species co-existence, answers to the {\{}‘Paradox{\}} of the Plankton'.},
-author = {Wilson, J. Bastow and Peet, Robert K. and Dengler, J{\"{u}}rgen and P{\"{a}}rtel, Meelis},
-doi = {10.1111/j.1654-1103.2012.01400.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilson et al. - 2012 - Plant species richness The world records.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {796--802},
-title = {{Plant species richness: The world records}},
-volume = {23},
-year = {2012}
-}
-@article{Bonal2007,
-abstract = {We characterised the among species variability in leaf gas exchange and morphological traits under controlled conditions of seedlings of 22 tropical rainforest canopy species to understand the origin of the variability in leaf carbon isotope discrimination ({\$}\backslashDelta{\$}) among species with different growth and dynamic characteristics (successional gradient). Our results first suggest that these species pursue a consistent strategy in terms of {\$}\backslashDelta{\$} throughout their ontogeny (juveniles grown here versus canopy adult trees from the natural forest). Second, leaf {\$}\backslashDelta{\$} was negatively correlated with WUE and N, and positively correlated with g{\$}{\_}{\{}\backslashrm s{\}}{\$}, but among species differences in {\$}\backslashDelta{\$} were mainly explained by differences in WUE. Finally, species belonging to different successional groups display distinct leaf functional and morphological traits. We confirmed that fast growing early successional species maximise carbon assimilation with high stomatal conductance. In contrast, fast and slow growing late successional species are both characterised by low carbon assimilation values, but by distinct stomatal conductance and leaf morphological features. Along the successional gradient, these differences result in much lower {\$}\backslashDelta{\$} for the intermediate species (i.e. fast growing late successional) as compared to the two other groups.},
-author = {Bonal, Damien and Born, C{\'{e}}line and Brechet, Claude and Coste, Sabrina and Marcon, Eric and Roggy, Jean-Christophe and Guehl, Jean-Marc},
-doi = {10.1051/forest:2006101},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonal et al. - 2007 - The successional status of tropical rainforest tree species is associated with differences in leaf carbon isotope.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {2},
-pages = {169--176},
-title = {{The successional status of tropical rainforest tree species is associated with differences in leaf carbon isotope discrimination and functional traits}},
-url = {http://www.afs-journal.org/articles/forest/abs/2007/02/f7018/f7018.html},
-volume = {64},
-year = {2007}
-}
-@incollection{Chao2016,
-abstract = {Conservation biologists need robust, intuitive mathematical tools to quantify and assess patterns and changes in biodiversity. Here we review some commonly used abundance-based species diversity measures and their phylogenetic generalizations. Most of the previous abundance-sensitive measures and their phylogenetic generalizations lack an essential property, the replication principle or doubling property. This often leads to inconsistent or counter-intuitive interpretations, especially in conservation applications. Hill numbers or the “effective number of species” obey the replication principle and thus resolve many of the interpretational problems. Hill numbers were recently extended to incorporate phylogeny; the resulting measures take into account phylogenetic differences between species while still satisfying the replication principle. We review the framework of phylogenetic diversity measures based on Hill numbers and their decomposition into independent alpha and beta components. Both additive and multiplicative decompositions lead to the same classes of normalized phylogenetic similarity or differentiation measures. These classes include multiple-assemblage phylogenetic generalizations of the Jaccard, S{\o}rensen, Horn and Morisita-Horn measures. For two assemblages, these classes also include the commonly used UniFrac and PhyloS{\o}r indices as special cases. Our approach provides a mathematically rigorous, self-consistent, ecologically meaningful set of tools for conservationists who must assess the phylogenetic diversity and complementarity of potential protected areas. Our framework is applied to a real dataset to illustrate (i) how to use phylogenetic diversity profiles to completely convey species abundances and phylogenetic information among species in an assemblage; and (ii) how to use phylogenetic similarity (or differentiation) profiles to assess phylogenetic resemblance or difference among multiple assemblages.},
-author = {Chao, Anne and Chiu, Chun-huo and Jost, Lou},
-booktitle = {Biodiversity Conservation and Phylogenetic Systematics},
-doi = {10.1007/978-3-319-22461-9},
-editor = {Pellens, Roseli and Grandcolas, Philippe},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu, Jost - 2016 - Phylogenetic Diversity Measures and Their Decomposition A Framework Based on Hill Numbers.pdf:pdf},
-isbn = {978-3-319-22460-2},
-pages = {141--172},
-publisher = {Springer Open},
-title = {{Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers}},
-url = {http://link.springer.com/10.1007/978-3-319-22461-9},
-volume = {14},
-year = {2016}
-}
-@article{Hausser2009,
-abstract = {We present a procedure for effective estimation of entropy and mutual information from smallsample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically as well as computationally. Despite its simplicity, we show that it outperforms eight other entropy estimation procedures across a diverse range of sampling scenarios and data-generating models, even in cases of severe undersampling. We illustrate the approach by analyzing E. coli gene expression data and computing an entropy-based gene-association network from gene expression data. A computer program is available that implements the proposed shrinkage estimator. {\textcopyright} 2009 Jean Hausser and Korbinian Strimmer.},
-annote = {Cited By (since 1996): 17
-Export Date: 15 November 2012
-Source: Scopus
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Hausser, Jean and Strimmer, Korbinian},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hausser, Strimmer - 2009 - Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks.pdf:pdf},
-journal = {Journal of Machine Learning Research},
-pages = {1469--1484},
-title = {{Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks}},
-url = {http://www.jmlr.org/papers/v10/hausser09a.html},
-volume = {10},
-year = {2009}
-}
-@article{Shem-Tov2017,
-abstract = {Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed or mainland-island scenarios. Here we combine analytic results and numerics to obtain an approximate solution for the species abundance distribution and the species richness for the neutral model on continuous landscape. We show how the regional diversity increases when the recruitment length decreases and the spatial segregation of species grows. Our results are supported by extensive numerical simulations and allow one to probe the numerically inaccessible regime of large-scale systems with extremely small mutation/speciation rates. Model predictions are compared with the findings of recent large-scale surveys of tropical trees across the Amazon basin, yielding new bounds for the species richness (between 13100 and 15000) and the number of singleton species (between 455 and 690).},
-author = {Shem-Tov, Yahav and Danino, Matan and Shnerb, Nadav M.},
-doi = {10.1038/srep42415},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shem-Tov, Danino, Shnerb - 2017 - Solution of the spatial neutral model yields new bounds on the Amazonian species richness.pdf:pdf},
-journal = {Scientific Reports},
-pages = {42415},
-title = {{Solution of the spatial neutral model yields new bounds on the Amazonian species richness}},
-url = {http://www.nature.com/articles/srep42415},
-volume = {7},
-year = {2017}
-}
-@article{Schurmann2004,
-abstract = {We consider the problem of finite sample corrections for entropy estimation. New estimates of the Shannon entropy are proposed and their systematic error (the bias) is computed analytically. We find that our results cover correction formulae of current entropy estimates recently discussed in the literature. The trade-off between bias reduction and the increase of the corresponding statistical error is analysed.},
-author = {Sch{\"{u}}rmann, Thomas},
-doi = {10.1088/0305-4470/37/27/L02},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sch{\"{u}}rmann - 2004 - Bias analysis in entropy estimation.pdf:pdf},
-journal = {Journal of Physics A: Mathematical and General},
-number = {27},
-pages = {L295--L301},
-title = {{Bias analysis in entropy estimation}},
-url = {http://stacks.iop.org/0305-4470/37/i=27/a=L02},
-volume = {37},
-year = {2004}
-}
-@article{Getzin2014,
-abstract = {The spatial placement of recruits around adult conspecifics represents the accumulated outcome of several pattern-forming processes and mechanisms such as primary and secondary seed dispersal, habitat associations or Janzen–Connell effects. Studying the adult–recruit relationship should therefore allow the derivation of specific hypotheses on the processes shaping population and community dynamics. We analysed adult–recruit associations for 65 tree species taken from six censuses of the 50 ha neotropical forest plot on Barro Colorado Island (BCI), Panama. We used point pattern analysis to test, at a range of neighbourhood scales, for spatial independence between recruits and adults, to assess the strength and type of departure from independence, and its relationship with species properties. Positive associations expected to prevail due to dispersal limitation occurred only in 16{\%} of all cases; instead a majority of species showed spatial ind pendence ({\~{}}73{\%}). Independence described the placement of recruits around conspecific adults in good approximation, although we found weak and noisy signals of species properties related to seed dispersal. We hypothesize that spatial mechanisms with strong stochastic components such as animal seed dispersal overpower the pattern-forming effects of dispersal limitation, density dependence and habitat association, or that some of the pattern-forming processes cancel out each other.},
-author = {Getzin, Stephan and Wiegand, Thorsten and Hubbell, Stephen P.},
-doi = {10.1098/rspb.2014.0922},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Getzin, Wiegand, Hubbell - 2014 - Stochastically driven adult-recruit associations of tree species on Barro Colorado Island.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {20140922},
-title = {{Stochastically driven adult-recruit associations of tree species on Barro Colorado Island}},
-volume = {281},
-year = {2014}
-}
-@article{Arbia2010,
-abstract = {The use of the K-functions (Ripley, 1977) has recently become popular in the analysis of the spatial pattern of firms. It was first introduced in the economic literature by Arbia and Espa (1996) and then popularized by Marcon and Puech (2003), Quah and Simpson (2003), Duranton and Overman (2005), and Arbia et al. (2008). In particular in Arbia et al. (2008) we used Ripley's K-functions as instruments to study the inter-sectoral co-agglomeration pattern of firms in a single moment of time. All this research has followed a static approach by disregarding the time dimension. Temporal dynamics, on the other hand, play a crucial role in understanding the economic and social phenomena particularly when referring to the analysis of the individual choices leading to the observed clusters of economic activities. With respect to previous contributions to the literature, this paper uncovers the process of firm demography by studying the dynamics of localization through space-time K-functions. The empirical part of the paper will focus on the study of the long run localization of firms in the area of Rome (Italy), by concentrating on the Information and Communication Technology (ICT) sector data collected by the Italian Industrial Union in the period 1920-2005. (C) 2009 Elsevier B.V. All rights reserved.},
-annote = {ISI Document Delivery No.: 644DB
-Times Cited: 0
-Cited Reference Count: 72
-Arbia, Giuseppe Espa, Giuseppe Giuliani, Diego Mazzitelli, Andrea
-2nd World Conference of the Spatial-Econometrics-Association (SEA)
-NOV, 2008
-New York, NY
-Spatial Econom Assoc
-ELSEVIER SCIENCE BV
-SI},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego and Mazzitelli, A.},
-doi = {10.1016/j.regsciurbeco.2009.10.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2010 - Detecting the existence of space-time clustering of firms.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {5},
-pages = {311--323},
-title = {{Detecting the existence of space-time clustering of firms}},
-volume = {40},
-year = {2010}
-}
-@article{Ho2009,
-abstract = {A very common way of analyzing different and complicated plant behaviors is to use spatial point pattern analysis, which allows us to assess whether there is any structure present. To test the complete spatial randomness hypothesis, Diggle (1979) proposed a Monte Carlo test whose test statistic is the discrepancy between the estimated and the theoretical form of some summary function, such as the Ripley K-function. In this article, we improve this test by adding various weight functions and get more powerful tests if decreasing and increasing weight functions are used for processes with short and long, respectively, range of interaction.},
-annote = {ISI Document Delivery No.: 383DV
-Times Cited: 0
-Cited Reference Count: 33
-Ho, Lai Ping Chiu, Sung Nok
-TAYLOR {\&} FRANCIS INC},
-author = {Ho, Lai Ping and Chiu, Sung Nok},
-doi = {10.1080/03610910802478343},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ho, Chiu - 2009 - Using Weight Functions in Spatial Point Pattern Analysis with Application to Plant Ecology Data.pdf:pdf},
-journal = {Communications in Statistics-Simulation and Computation},
-number = {2},
-pages = {269--287},
-title = {{Using Weight Functions in Spatial Point Pattern Analysis with Application to Plant Ecology Data}},
-url = {http://www.tandfonline.com/doi/full/10.1080/03610910802478343},
-volume = {38},
-year = {2009}
-}
-@article{Chazdon2016,
-abstract = {We present a historical overview of forest concepts and definitions, linking these changes with distinct perspectives and management objectives. Policies dealing with a broad range of forest issues are often based on definitions created for the purpose of assessing global forest stocks, which do not distinguish between natural and planted forests or reforests, and which have not proved useful in assessing national and global rates of forest regrowth and restoration. Implementing and monitoring forest and landscape restoration requires additional approaches to defining and assessing forests that reveal the qualities and trajectories of forest patches in a spatially and temporally dynamic landscape matrix. New technologies and participatory assessment of forest states and trajectories offer the potential to operationalize such definitions. Purpose-built and contextualized definitions are needed to support policies that successfully protect, sustain, and regrow forests at national and global scales. We provide a framework to illustrate how different management objectives drive the relative importance of different aspects of forest state, dynamics, and landscape context.},
-author = {Chazdon, Robin L. and Brancalion, Pedro H. S. and Laestadius, Lars and Bennett-Curry, Aoife and Buckingham, Kathleen and Kumar, Chetan and Moll-Rocek, Julian and {Guimar{\~{a}}es Vieira}, Ima C{\'{e}}lia and Wilson, Sarah Jane},
-doi = {10.1007/s13280-016-0772-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chazdon et al. - 2016 - When is a forest a forest Forest concepts and definitions in the era of forest and landscape restoration.pdf:pdf},
-journal = {Ambio},
-number = {5},
-pages = {538--550},
-title = {{When is a forest a forest? Forest concepts and definitions in the era of forest and landscape restoration}},
-url = {https://link.springer.com/article/10.1007/s13280-016-0772-y},
-volume = {45},
-year = {2016}
-}
-@article{Smith1977,
-abstract = {A family ofspecies diversity measures proposed by Hurlbert ( 1971) is defined as the expected number of species in a random sample of m individuals from a population. For m = 2 this measure is equivalent to Simpson's diversity index. For larger m, the measure is increasingly sensitive to rare species. In this paper we use unbiased estimation theory to obtain a minimum variance unbiased estimator for this family of diversity measures. An unbiased estimator of the sampling variance is also obtained. These results are then used to partition the variation in sample diversity between random sampling error and local variation community diversity.},
-author = {Smith, Woollcott and Grassle, J. Frederick},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith, Grassle - 1977 - Sampling properties of a family of diversity measures.pdf:pdf},
-journal = {Biometrics},
-number = {2},
-pages = {283--292},
-title = {{Sampling properties of a family of diversity measures}},
-url = {http://www.jstor.org/stable/2529778},
-volume = {33},
-year = {1977}
-}
-@article{Pavoine2009b,
-abstract = {Functional diversity is at the heart of current research in the field of conservation biology. Most of the indices that measure diversity depend on variables that have various statistical types (e.g. circular, fuzzy, ordinal) and that go through a matrix of distances among species. We show how to compute such distances from a generalization of Gower's distance, which is dedicated to the treatment of mixed data. We prove Gower's distance can be extended to include new types of data. The impact of this generalization is illustrated on a real data set containing 80 plant species and 13 various traits. Gower's distance allows an efficient treatment of missing data and the inclusion of variable weights. An evaluation of the real contribution of each variable to the mixed distance is proposed. We conclude that such a generalized index will be crucial for analyzing functional diversity at small and large scales. The},
-author = {Pavoine, Sandrine and Vallet, Jeanne and Dufour, Anne-B{\'{e}}atrice and Gachet, Sophie and Daniel, Herv{\'{e}}},
-doi = {10.1111/j.1600-0706.2009.16668.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine et al. - 2009 - On the challenge of treating various types of variables application for improving the measurement of functional.pdf:pdf},
-journal = {Oikos},
-number = {3},
-pages = {391--402},
-title = {{On the challenge of treating various types of variables: application for improving the measurement of functional diversity}},
-url = {http://doi.wiley.com/10.1111/j.1600-0706.2009.16668.x},
-volume = {118},
-year = {2009}
-}
-@article{Nei1973,
-author = {Nei, Masatoshi},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nei - 1973 - Analysis of Gene Diversity in Subdivided Populations.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {12},
-pages = {3321--3323},
-title = {{Analysis of Gene Diversity in Subdivided Populations}},
-volume = {70},
-year = {1973}
-}
-@article{Kraft2015,
-abstract = {1. One of the most pervasive concepts in the study of community assembly is the metaphor of the environmental filter, which refers to abiotic factors that prevent the establishment or persistence of species in a particular location. The metaphor has its origins in the study of community change during succession and in plant community dynamics, although it has gained considerable attention recently as part of a surge of interest in functional trait and phylogenetic-based approaches to the study of communities. 2. While the filtering metaphor has clear utility in some circumstances, it has been challenging to reconcile the environmental filtering concept with recent developments in ecological theory related to species coexistence. These advances suggest that the evidence used in many studies to assess environmental filtering is insufficient to distinguish filtering from the outcome of biotic interactions. 3. We re-examine the environmental filtering metaphor from the perspective of coexistence theory. In an effort to move the discussion forward, we present a simple framework for considering the role of the environment in shaping community membership, review the literature to document the evidence typically used in environmental filtering studies and highlight research challenges to address in coming years. 4. The current usage of the environmental filtering term in empirical studies likely overstates the role abiotic tolerances play in shaping community structure. We recommend that the term ‘environmental filtering' only be used to refer to cases where the abiotic environment prevents establishment or persistence in the absence of biotic interactions, although only 15{\%} of the studies in our review presented such evidence. Finally, we urge community ecologists to consider additional mechanisms aside from environmental filtering by which the abiotic environment can shape community pattern.},
-author = {Kraft, Nathan J. B. and Adler, Peter B. and Godoy, Oscar and James, Emily C. and Fuller, Steve and Levine, Jonathan M.},
-doi = {10.1111/1365-2435.12345},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kraft et al. - 2015 - Community assembly, coexistence and the environmental filtering metaphor.pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {592--599},
-title = {{Community assembly, coexistence and the environmental filtering metaphor}},
-url = {http://doi.wiley.com/10.1111/1365-2435.12345},
-volume = {29},
-year = {2015}
-}
-@article{Kosfeld2011,
-abstract = {Traditional measures of spatial industry concentration are restricted to given areal units. They do not make allowance for the fact that concentration may be differently pronounced at various geographical levels. Methods of spatial point pattern analysis allow one to measure industry concentration at a continuum of spatial scales. While common distance-based methods are well applicable for sub-national study areas, they become inefficient in measuring concentration at various levels within industrial countries. This particularly applies in testing for conditional concentration where overall manufacturing is used as a reference population. Using Ripley's K function approach to second-order analysis, we propose a subsample similarity test as a feasible testing approach for establishing conditional clustering or dispersion at different spatial scales. For measuring the extent of clustering and dispersion, we introduce a concentration index of the style of Besag's (J R Stat Soc B, 25:294, 1977) L function. The new index can be employed to measure the extent of substantial clustering and dispersion. The K function approach is employed to identifying measuring industry concentration in Germany.},
-author = {Kosfeld, Reinhold and Eckey, Hans-Friedrich and Lauridsen, J{\o}rgen},
-doi = {10.1007/s00168-010-0385-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosfeld, Eckey, Lauridsen - 2011 - Spatial point pattern analysis and industry concentration.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {2},
-pages = {311--328},
-title = {{Spatial point pattern analysis and industry concentration}},
-url = {http://dx.doi.org/10.1007/s00168-010-0385-5},
-volume = {47},
-year = {2011}
-}
-@incollection{Prance1977,
-author = {Prance, G T},
-booktitle = {Extinction Is Forever},
-isbn = {532; TY - JOUR RP - Not In File; EndNote database},
-pages = {195--213},
-title = {{The Phytogeographic Subdivisions of Amazonia and Their Influence on the Selection of Biological Reserves}},
-year = {1977}
-}
-@article{Haase1997,
-abstract = {Univariate and bivariate distribution patterns of small shrubs on abandoned land in semi-arid southeastern Spain were investigated by second-order spatial analysis (Ripley's K- function). All shrubs (Anthyllis cytisoides and subdominant Artemisia barrelieri) were either randomly distributed or clumped at scales of 0.25-1.0 m. The pattern shown by A. cytisoides shrubs alone changed from clumped to random with decreasing density. Pattern analysis and demographic data suggest a successive replacement of A. barrelieri, which had high proportions (44-86{\%}) of dead shrubs, by the dominant A. cytisoides. In two of three plots there was a positive association between A. cytisoides and A. barrelieri at a scale of 0.25-0.5 m. In the third plot, believed to represent a more advanced stage of colonization, there was a negative association (repulsion) between the two species, presumably as a result of interspecific competition from A. cytisoides. Dead shrubs present in spring 1994 were randomly distributed in all plots. Living and dead A. cytisoides shrubs were positively associated at a scale of 0.5 m, suggesting that the shrubs died as a result of intraspecific competition in small clumps. The shrubland previously dominated by A. barrelieri is changing to A. cytisoides shrubland with increasing biomass and ground cover.},
-author = {Haase, Peter and Pugnaire, Francisco I. and Clark, S. C. and Incoll, L. D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haase et al. - 1996 - Spatial patterns in a two-tiered semi-arid shrubland in southeastern Spain.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {5},
-pages = {627--634},
-title = {{Spatial pattern in Anthyllis cytisoides shrubland on abandoned land in southeastern Spain}},
-volume = {8},
-year = {1997}
-}
-@book{Silverman1986,
-address = {London},
-author = {Silverman, B. W.},
-pages = {1--175},
-publisher = {Chapman and Hall},
-title = {{Density estimation for statistics and data analysis}},
-year = {1986}
-}
-@article{Tsallis2004,
-abstract = {Boltzmann-Gibbs statistical mechanics is based on the entropy S-BG = -k Sigma(i=1)(W) p(i) ln p(i). It enables a successful thermal approach to ubiquitous systems, such as those involving short-range interactions, markovian processes, and, generally speaking, those systems whose dynamical occupancy of phase space tends to be ergodic. For systems whose microscopic dynamics is more complex, it is natural to expect that the dynamical occupancy of phase space will have a less trivial structure, for example a (multi)fractal or hierarchical geometry. The question naturally arises whether it is possible to study such systems with concepts and methods similar to those of standard statistical mechanics. The answer appears to be yes for ubiquitous systems, but the concept of entropy needs to be adequately generalized. Some classes of such systems can be satisfactorily approached with the entropy S-q = k(1-Sigmai=1W piq)/q(-1) (with q is an element of R, and S-1 = S-BG). This theory is sometimes referred in the literature as nonextensive statistical mechanics. We provide here a brief introduction to the formalism, its dynamical foundations, and some illustrative applications. In addition to these, we illustrate with a few examples the concept of stability (or experimental robustness) introduced by B. Lesche in 1982 and recently revisited by S. Abe.},
-annote = {ISI Document Delivery No.: 800UU
-Times Cited: 42
-Cited Reference Count: 103
-SPRINGER-VERLAG},
-author = {Tsallis, Constantino and Brigatti, E.},
-doi = {10.1007/s00161-004-0174-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsallis, Brigatti - 2004 - Nonextensive statistical mechanics A brief introduction.pdf:pdf},
-journal = {Continuum Mechanics and Thermodynamics},
-number = {3},
-pages = {223--235},
-title = {{Nonextensive statistical mechanics: A brief introduction}},
-url = {http://link.springer.com/article/10.1007/s00161-004-0174-4},
-volume = {16},
-year = {2004}
-}
-@article{Grunwald2010,
-abstract = {The elementary theories of Shannon information and Kolmogorov complexity are compared, the extent to which they have a common purpose, and where they are fundamentally different. The focus is on: Shannon entropy versus Kolmogorov complexity, the relation of both to universal coding, Shannon mu- tual information versus Kolmogorov (‘algorithmic') mutual information, probabilistic sufficient statistic versus algorithmic sufficient statistic (related to lossy compression in the Shannon theory versus mean- ingful information in the Kolmogorov theory), and rate distortion theory versus Kolmogorov's structure function. Part of the material has appeared in print before, scattered through various publications, but this is the first comprehensive systematic comparison. The last mentioned relations are new.},
-author = {Gr{\"{u}}nwald, Peter and Vit{\'{a}}nyi, Paul},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gr{\"{u}}nwald, Vit{\'{a}}nyi - 2010 - Shannon Information and Kolmogorov Complexity.pdf:pdf},
-journal = {arXiv},
-number = {v.2010-07-22},
-title = {{Shannon Information and Kolmogorov Complexity}},
-volume = {0410002},
-year = {2010}
-}
-@article{Loreau2001b,
-abstract = {The ecological consequences of biodiversity loss have aroused considerable interest and controversy during the past decade. Major advances have been made in describing the relationship between species diversity and ecosystem processes, in identifying functionally important species, and in revealing underlying mechanisms. There is, however, uncertainty as to how results obtained in recent experiments scale up to landscape and regional levels and generalize across ecosystem types and processes. Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments. A major future challenge is to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.},
-author = {Loreau, Michel and Naeem, Shahid and Inchausti, Pablo and Bengtsson, J. and Grime, J. P. and Hector, Andrew and Hooper, David U. and Huston, M. A. and Raffaelli, D. and Schmid, B. and Tilman, David and Wardle, David A.},
-doi = {10.1126/science.1064088},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau et al. - 2001 - Biodiversity and ecosystem functioning current knowledge and future challenges.pdf:pdf},
-journal = {Science},
-number = {5543},
-pages = {804--808},
-title = {{Biodiversity and ecosystem functioning: current knowledge and future challenges.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/11679658},
-volume = {294},
-year = {2001}
-}
-@book{Krugman1991,
-address = {London},
-annote = {Disponible : Chap. 2 seulement},
-author = {Krugman, Paul},
-publisher = {MIT Press},
-title = {{Geography and Trade}},
-year = {1991}
-}
-@article{Kerr2015,
-abstract = {We model spatial clusters of similar firms. Our model highlights how agglomerative forces lead to localized, individual connections among firms, while interaction costs generate a defined distance over which attraction forces operate. Overlapping firm interactions yield agglomera-tion clusters that are much larger than the underlying agglomerative forces themselves. Empirically, we demonstrate that our model's assumptions are present in the structure of technology and labor flows within SiliconValley. Our model further identifies how the lengths over which agglomerative forces operate influence the shapes and sizes of industrial clusters; we confirm these predictions using variations across patent technology clusters.},
-author = {Kerr, William R. and Kominers, Scott Duke},
-doi = {10.1162/REST_a_00471},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kerr, Kominers - 2015 - Agglomerative Forces and Cluster Shapes.pdf:pdf},
-journal = {Review of Economics and Statistics},
-month = {oct},
-number = {4},
-pages = {877--899},
-title = {{Agglomerative Forces and Cluster Shapes}},
-url = {http://www.mitpressjournals.org/doi/10.1162/REST{\_}a{\_}00471},
-volume = {97},
-year = {2015}
-}
-@book{Centretechniqueforestiertropical1989,
-author = {Centre technique forestier tropical},
-isbn = {978-2-85411-008-1},
-publisher = {Cirad},
-title = {{Bois des DOM-TOM}},
-url = {http://www.quae.com/fr/r1002-bois-des-dom-tom-t1-guyane.html},
-volume = {1:Guyane},
-year = {1989}
-}
-@book{Moller2004,
-author = {M{\o}ller, Jesper and Waagepetersen, Rasmus Plenge},
-booktitle = {Monographs on Statistics and Applies Probabilities},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/M{\o}ller, Waagepetersen - 2004 - Statistical Inference and Simulation for Spatial Point Processes.pdf:pdf},
-pages = {1--300},
-publisher = {Chapman and Hall},
-title = {{Statistical Inference and Simulation for Spatial Point Processes}},
-volume = {100},
-year = {2004}
-}
-@article{Rosenthal2003,
-abstract = {This paper makes two contributions to the empirical literature on agglomeration economies. First, the paper uses a unique and rich database in conjunction with mapping software to measure the geographic extent of agglomerative externalities. Previous papers have been forced to assume that agglomeration economies are club goods that operate at a metropolitan scale. Second, the paper tests for the existence of organizational agglomeration economies of the kind studied qualitatively by Saxenian (1994). This is a potentially important source of increasing returns that previous empirical work has not considered. Results indicate that localization economies attenuate rapidly and that industrial organization affects the benefits of agglomeration.},
-author = {Rosenthal, Stuart S. and Strange, William C.},
-doi = {10.1162/003465303765299882},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rosenthal, Strange - 2003 - Geography, Industrial Organisation, and Agglomeration.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {2},
-pages = {377--393},
-title = {{Geography, Industrial Organisation, and Agglomeration}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/003465303765299882?journalCode=rest},
-volume = {85},
-year = {2003}
-}
-@article{Forget1997,
-abstract = {The seedling shadow is described of a frugivore (spider monkey [Ateles paniscus]) dispersed species of Virola (a new species to be described elsewhere) in rain forest at the Nouragues Biological Reserve in French Guiana, and data are presented and discussed from a 4-yr (October 1984 to November 1988) study of seedling dynamics. The forest is undisturbed with an intact and abundant fauna, especially of primates. The new Virola sp. is a large canopy tree which may reach {\textgreater}50 m in height and {\textgreater}100 cm in diameter, and it flowers and fruits annually. Fruit dispersal by spider monkeys leads to aggregated or sparse patterns of seedling populations, depending on whether the dispersal was clumped or scattered. Seedling recruitment is abundant because there is little post-dispersal predation/parasitism. There was no apparent parent-offspring conflict due to the abundant seedling population close to the parent over the 4-yr study, but a peak of recruitment occurred at 20-60 m from the parent (in accordance with the Janzen- Connell model).},
-author = {Forget, Pierre-Michel and Sabatier, Daniel},
-doi = {10.1017/S0266467400010920},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Forget, Sabatier - 1997 - Dynamics of the seedling shadow of a frugivore-dispersed tree species in French Guiana.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {5},
-pages = {767--773},
-title = {{Dynamics of the seedling shadow of a frugivore-dispersed tree species in French Guiana}},
-url = {https://www.cambridge.org/core/journals/journal-of-tropical-ecology/article/dynamics-of-the-seedling-shadow-of-a-frugivoredispersed-tree-species-in-french-guiana/97E9C67EB63701B9BD28BB259EFFE826},
-volume = {13},
-year = {1997}
-}
-@article{Sweeney2005,
-abstract = {Administrative data sources are increasingly being used for spatial analysis and policy formation. For example, 'welfare to work' programs have stimulated demand for spatial mismatch studies in which ES-202 employment files are used. The increased resolution gained by geocoding the address records in administrative files can be of enormous research value when the process under study resolves over small distances. Yet the resulting point-referenced data are problematic for inferential analysis. In particular, administrative data typically represent a sample of convenience, thus posing serious validity problems for statistical inference. The authors propose a robust estimation method for spatial pattern inference based on spatially censored data. The performance of the estimator is explored with the aid of simulated data and is also demonstrated with ES-202 data from North Carolina.},
-author = {Sweeney, Stuart H. and Konty, Kevin J.},
-doi = {10.1068/a35318},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sweeney, Konty - 2005 - Robust point-pattern inference from spatially censored data.pdf:pdf},
-journal = {Environment and Planning A},
-number = {1},
-pages = {141--159},
-title = {{Robust point-pattern inference from spatially censored data}},
-url = {http://journals.sagepub.com/doi/abs/10.1068/a35318},
-volume = {37},
-year = {2005}
-}
-@article{Ceriani2012,
-abstract = {The scope of this paper is to celebrate the 100th anniversary of the Gini index by providing the original formulae. Corrado Gini introduced his index for the first time in a 1912 book published in Italian under the name of Variabilit{\`{a}} e Mutabilit{\`{a}} (Variability and Mutability). This article provides selected extracts of Part I of the book dedicated to measures of variability. We find that Gini proposed no less than 13 formulations of his index, none of which is known today to the large public. We also find that Gini anticipated some of the developments that derived from the study of his index.},
-author = {Ceriani, Lidia and Verme, Paolo},
-doi = {10.1007/s10888-011-9188-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ceriani, Verme - 2012 - The origins of the Gini index extracts from Variabilit{\`{a}} e Mutabilit{\`{a}} (1912) by Corrado Gini.pdf:pdf},
-journal = {Journal of Economic Inequality},
-number = {3},
-pages = {421--443},
-title = {{The origins of the Gini index: extracts from Variabilit{\`{a}} e Mutabilit{\`{a}} (1912) by Corrado Gini}},
-url = {http://dx.doi.org/10.1007/s10888-011-9188-x},
-volume = {10},
-year = {2012}
-}
-@article{Zhang2006,
-abstract = {Knowing the global pattern of species diversity is a central goal of the science of ecology, and scaling laws can be useful for analysis of cross-scale biodiversity patterns. An elevational gradient in a warm temperate zone of the Donglingshan mountains (China) is used to test the scaling laws of species abundance distribution using multifractal analysis.We show that the power law scaling relationship holds for not just the classical SAR (speciesarea relationship for richness), but also for Shannon and Simpson diversity. In fact, we find power-laws in the generalized species abundance distribution at all stratal levels of the forest (trees, shrubs and herbs). The fact that these laws exist across a heterogeneous landscape representing a strong bioclimatic gradient suggests that biodiversity scaling laws may be more robust than previously thought.},
-author = {Zhang, Yuxin and Ma, Keming and Anand, Madhur and Fu, Bojie},
-doi = {10.1111/j.2006.0030-1299.15021.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang et al. - 2006 - Do generalized scaling laws exist for species abundance distribution in mountains.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {81--88},
-title = {{Do generalized scaling laws exist for species abundance distribution in mountains?}},
-volume = {115},
-year = {2006}
-}
-@article{Chao2017a,
-abstract = {In the context of capture-recapture studies, Chao (1987) derived an inequality among capture frequency counts to obtain a lower bound for the size of a population based on individuals' capture/non-capture records for multiple capture occasions. The inequality has been applied to obtain a non-parametric lower bound of species richness of an assemblage based on species incidence (detection/non-detection) data in multiple sampling units. The inequality implies that the number of undetected species can be inferred from the species incidence frequency counts of the uniques (species detected in only one sampling unit) and duplicates (species detected in exactly two sampling units). In their pioneering paper, Colwell and Coddington (1994) gave the name “Chao2” to the estimator for the resulting species richness. (The “Chao1” estimator refers to a similar type of estimator based on species abundance data). Since then, the Chao2 estimator has been applied to many research fields and led to fruitful generalizations. Here, we first review Chao's inequality under various models and discuss some related statistical inference questions: (1) Under what conditions is the Chao2 estimator an unbiased point estimator? (2) How many additional sampling units are needed to detect any arbitrary proportion (including 100{\%}) of the Chao2 estimate of asymptotic species richness? (3) Can other incidence frequency counts be used to obtain similar lower bounds? We then show how the Chao2 estimator can be also used to guide a non-asymptotic analysis in which species richness estimators can be compared for equally-large or equally-complete samples via sample-size-based and coverage-based rarefaction and extrapolation. We also review the generalization of Chao's inequality to estimate species richness under other sampling-without-replacement schemes (e.g. a set of quadrats, each surveyed only once), to obtain a lower bound of undetected species shared between two or multiple assemblages, and to allow inferences about undetected phylogenetic richness (the total length of undetected branches of a phylogenetic tree connecting all species), with associated rarefaction and extrapolation. A small empirical dataset for Australian birds is used for illustration, using online software SpadeR, iNEXT, and PhD.},
-author = {Chao, Anne and Colwell, Robert K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Colwell - 2017 - Thirty years of progeny from Chao's inequality Estimating and comparing richness with incidence data and incomple.pdf:pdf},
-journal = {SORT-Statistics and Operations Research Transactions},
-number = {1},
-pages = {3--54},
-title = {{Thirty years of progeny from Chao's inequality: Estimating and comparing richness with incidence data and incomplete sampling}},
-url = {http://www.raco.cat/index.php/SORT/article/view/326047},
-volume = {41},
-year = {2017}
-}
-@article{Bellwood2003,
-abstract = {Biodiversity is frequently associated with functional redundancy. Indo-Pacific coral reefs incorporate some of the most diverse ecosystems on the globe with over 3000 species of fishes recorded from the region. Despite this diversity, we document changes in ecosystem function on coral reefs at regional biogeographical scales as a result of overfishing of just one species, the giant humphead parrotfish (Bolbometopon muricatum ). Each parrotfish ingests over 5 tonnes of structural reef carbonates per year, almost half being living corals. On relatively unexploited oceanic reefs, total ingestion rates per m(2) balance estimated rates of reef growth. However, human activity and ecosystem disruption are strongly correlated, regardless of local fish biodiversity. The results emphasize the need to consider the functional role of species when formulating management strategies and the potential weakness of the link between biodiversity and ecosystem resilience.},
-author = {Bellwood, David R. and Hoey, A. S. and Choat, J .H.},
-doi = {10.1046/j.1461-0248.2003.00432.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bellwood, Hoey, Choat - 2003 - Limited functional redundancy in high diversity systems resilience and ecosystem function on coral reefs.pdf:pdf},
-journal = {Ecology Letters},
-number = {4},
-pages = {281--285},
-title = {{Limited functional redundancy in high diversity systems: resilience and ecosystem function on coral reefs}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00432.x/abstract},
-volume = {6},
-year = {2003}
-}
-@article{Giuliani2014,
-abstract = {The spatial concentration of firms has long been a central issue in economics under both the theoretical and the applied point of view mainly due to the important policy implications. A popular approach to its measurement, which does not suffer from the problem of the arbitrariness of the regional boundaries, makes use of micro data and looks at the firms as if they were dimensionless points distributed in the economic space. However, in practical circumstances the points (firms) observed in the economic space are far from being dimensionless and are conversely characterized by different dimension in terms of the number of employees, the product, the capital, and so on. In the literature, the works that originally introduce such an approach disregard the aspect of the different firm dimension and ignore the fact that a high degree of spatial concentration may result from the case of both many small points clustering in definite portions of space and only few large points clustering together (e.g., few large firms). We refer to this phenomenon as clustering of firms and clustering of economic activities. The present article aims at tackling this problem by adapting the popular K-function to account for the point dimension using the framework of marked point process theory.},
-author = {Giuliani, Diego and Arbia, Giuseppe and Espa, Giuseppe},
-doi = {10.1177/0160017612461357},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Giuliani, Arbia, Espa - 2014 - Weighting Ripley's K-Function to Account for the Firm Dimension in the Analysis of Spatial Concentration.pdf:pdf},
-journal = {International Regional Science Review},
-number = {3},
-pages = {251--272},
-title = {{Weighting Ripley's K-Function to Account for the Firm Dimension in the Analysis of Spatial Concentration}},
-url = {http://irx.sagepub.com/content/early/2012/10/11/0160017612461357.abstract},
-volume = {37},
-year = {2014}
-}
-@article{DeDominicis2013,
-abstract = {De Dominicis L., Arbia G. and De Groot H. L. F. Concentration of manufacturing and service sector activities in Italy: accounting for spatial dependence and firm size distribution, Regional Studies. Empirical analysis of the spatial distribution of economic activity on a discrete space is based on measures that suffer from a series of drawbacks. A methodological advance is proposed here in two respects. First, the analysis is extended to take spatial dependence explicitly into account. Second, differences in the size distribution of firms between territorial units are controlled for. Using data for Italy, exploratory spatial data analysis is applied to identify sectoral location patterns in both the manufacturing industry as well as the business services. It is found that large differences prevail in the geographical concentration of production across sectors.},
-annote = {ISI Document Delivery No.: 105KC
-Times Cited: 1
-Cited Reference Count: 39
-De Dominicis, Laura Arbia, Giuseppe De Groot, Henri L. F.
-Routledge journals, taylor {\&} francis ltd
-Abingdon
-Si},
-author = {{De Dominicis}, L. and Arbia, Giuseppe and {De Groot}, H. L. F.},
-doi = {10.1080/00343404.2011.579593},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/De Dominicis, Arbia, De Groot - 2013 - Concentration of Manufacturing and Service Sector Activities in Italy Accounting for Spatial Depe.pdf:pdf},
-journal = {Regional Studies},
-number = {3},
-pages = {405--418},
-title = {{Concentration of Manufacturing and Service Sector Activities in Italy: Accounting for Spatial Dependence and Firm Size Distribution}},
-url = {http://www.tandfonline.com/doi/pdf/10.1080/00343404.2011.579593},
-volume = {47},
-year = {2013}
-}
-@article{Mizera2003,
-abstract = {In this study, we examine the ecology and adaptive dynamics of an asexually reproducing population, migrating along an environmental gradient. The living conditions are optimal at the central location and deteriorate outwards. The different strategies are optimized to the ecological conditions of different locations. The control parameters are the migration and the tolerance of the strategies towards the environmental condition (location). Locally, population growth is logistic and selection is frequency-independent, corresponding to the case of a single limiting resource. The behaviour of the population is modelled by numerically integrated reaction-diffusion equations as well as by individual-based simulations. Limiting similarity, spatial niche segregation and character displacement are demonstrated, analogous to resource-heterogeneity based niche partitioning. Pairwise invasibility analysis reveals a convergent stable singular strategy optimized to the central, optimal location. It is evolutionarily stable if the migration rate and the tolerance are large. Decreasing migration or decreasing tolerance bifurcates the singular strategy to an evolutionary branching point. Individual-based simulation of evolution confirms that, in the case of branching singularity, evolution converges to this singular strategy and branches there. Depending on the environmental tolerance, further branching may occur. The branching evolution in the asexual model is interpreted as a sign that the ecology of an environmental gradient is prone to adaptive geographic speciation.},
-author = {Mizera, Ferenc and Mesz{\'{e}}na, G{\'{e}}za},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mizera, Mesz{\'{e}}na - 2003 - Spatial niche packing, character displacement and adaptive speciation along an environmental gradient.pdf:pdf},
-journal = {Evolutionary Ecology Research},
-pages = {363--382},
-title = {{Spatial niche packing, character displacement and adaptive speciation along an environmental gradient}},
-url = {http://www.evolutionary-ecology.com/abstracts/v05/1489.html},
-volume = {5},
-year = {2003}
-}
-@article{Scholl2015,
-abstract = {Distance-based methods for measuring spatial concentration of indus- tries have received an increasing popularity in the spatial econometrics community. However, a limiting factor for using these methods is their computational com- plexity since both their memory requirements and running times are in O(n²).In this paper, we present an algorithm with constant memory requirements and shorter running time, enabling distance-based methods to deal with large data sets. We discuss three recent distance-based methods in spatial econometrics: the D{\&}O- Index by Duranton and Overman (Rev Econ Stud 72(4):1077–1106, 2005), the M- function by Marcon and Puech (J Econ Geogr 10(5):745–762, 2010) and the Cluster-Index by Scholl and Brenner (Reg Stud (ahead-of-print):1–15, 2014). Finally, we present an alternative calculation for the latter index that allows the use of data sets with millions of firms. Keywords},
-author = {Scholl, Tobias and Brenner, Thomas},
-doi = {10.1007/s10109-015-0219-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scholl, Brenner - 2015 - Optimizing distance-based methods for large data sets.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {4},
-pages = {333--351},
-title = {{Optimizing distance-based methods for large data sets}},
-url = {http://link.springer.com/article/10.1007/s10109-015-0219-1{\#}},
-volume = {17},
-year = {2015}
-}
-@incollection{Catin1994,
-address = {Paris},
-author = {Catin, Maurice},
-booktitle = {Encyclop{\'{e}}die d'Economie Spatiale},
-editor = {Audray, Jean-Paul and Bailly, Antoine and Derycke, Pierre-Henri and Huriot, Jean-Marie},
-pages = {99--103},
-publisher = {Economica},
-title = {{Externalit{\'{e}}s}},
-volume = {Chapitre 1},
-year = {1994}
-}
-@article{Case1991,
-abstract = {In this paper I discuss economic processes that may give rise to spatial patterns in data, and explore the relative merits of alternative modeling approaches when data are spatially correlated. Specifically, I present an estimation scheme that allows for spatial random effects, and focus attention on cases in which such a framework may be preferred to the more general fixed effects framework that nests it. I use the models presented, together with information on the location of households in an Indonesian socio-economic survey, to test spatial relationships in Indonesian demand for rice.},
-author = {Case, Anne C.},
-doi = {0012-9682(199107)59:4<953:SPIHD>2.0.CO;2-Z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Case - 1991 - Spatial Patterns in Household Demand.pdf:pdf},
-journal = {Econometrica},
-number = {4},
-pages = {953--965},
-title = {{Spatial Patterns in Household Demand}},
-url = {https://www.econometricsociety.org/publications/econometrica/1991/07/01/spatial-patterns-household-demand},
-volume = {59},
-year = {1991}
-}
-@misc{IGN2002,
-author = {IGN},
-keywords = {Coordonn{\'{e}}es,IGN (2002).pdf,Lambert},
-mendeley-tags = {IGN (2002).pdf},
-pages = {13 p.},
-title = {{Transformation entre syst{\`{e}}mes g{\'{e}}od{\'{e}}siques}},
-url = {http://www.ign.fr/fr/PI/activites/geodesie/rgf93/OUTILS},
-year = {2002}
-}
-@article{Marcon2010,
-abstract = {We discuss a property of distance-based measures that has not been addressed with regard to evaluating the geographic concentration of economic activities. The article focuses on the choice between a probability density function of point-pair distances or a cumulative function. We begin by introducing a new cumulative function, M, for evaluating the relative geographic concentration and the co-location of industries in a non-homogeneous spatial framework. Secondly, some rigorous comparisons are made with the leading probability density function of Duranton and Overman (2005), Kd. The merits of the simultaneous use of Kd and M is proved, underlining the complementary nature of the results they provide.},
-author = {Marcon, Eric and Puech, Florence},
-doi = {10.1093/jeg/lbp056},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech - 2010 - Measures of the Geographic Concentration of Industries Improving Distance-Based Methods.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {5},
-pages = {745--762},
-title = {{Measures of the Geographic Concentration of Industries: Improving Distance-Based Methods}},
-url = {http://joeg.oxfordjournals.org/content/early/2009/11/26/jeg.lbp056},
-volume = {10},
-year = {2010}
-}
-@article{Carranza2007,
-abstract = {This paper analyses the use of R{\`{e}}nyi's generalized entropy function to identify landscape temporal transformation. In order to demonstrate its application we analyze recent historic landscape diversity changes focusing on the evolution of boundaries between patches in the town of Isernia (central Italy). Firstly, three 1:25,000 land cover/vegetation raster maps (1954, 1981 and 1992) were selected. Next, changes in landscape diversity were measured analyzing the variation in the extension of boundary types between adjacent land cover categories (patches) from 1954 to 1992. To do this, R{\`{e}}nyi's diversity curves for each year were built and compared. The major advantage in applying the R{\`{e}}nyi generalized parametric diversity function to analyze landscape changes in time is that diversity profiles do not display a single index. In fact, a family of indexes is shown, many of which are currently applied and widely used in landscape ecology. {\textcopyright} 2006 Elsevier Ltd. All rights reserved.},
-annote = {Cited By (since 1996):13
-Export Date: 12 March 2014
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Carranza, M.L.; Dip. S.T.A.T., Faculty of Mathematics, Physics and Natural Sciences, Via Mazzini 8, I-86170 Isernia, Italy; email: carranza@unimol.it},
-author = {Carranza, M. L. and Acosta, Alicia T.R. and Ricotta, Carlo},
-doi = {10.1016/j.ecolind.2006.05.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carranza, Acosta, Ricotta - 2007 - Analyzing landscape diversity in time The use of R{\`{e}}nyi's generalized entropy function.pdf:pdf},
-journal = {Ecological Indicators},
-number = {3},
-pages = {505--510},
-title = {{Analyzing landscape diversity in time: The use of R{\`{e}}nyi's generalized entropy function}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33947624176{\&}partnerID=40{\&}md5=6e46204c8598895ef252d74f7ba27704},
-volume = {7},
-year = {2007}
-}
-@article{Sabatier1997,
-abstract = {The impact of soil cover organization on the forest community was studied in a 19 ha tract at Piste de St Elie station in French Guiana. One hundred and ninety five species, each represented by at least 10 individuals, were chosen from records of the position, diameter at breast height (dbh) and precise identification by botanical sampling of 12 104 ligneous plants (dbh more than or equal to 10 cm). Spatial variations in the soil were mapped using the method proposed by Boulet et al. (1982). The soil mapping units corresponded to the successive stages of evolution of a currently unbalanced ferralitic cover. These stages described firstly the thinning by erosion of the micro-aggregate d upper horizon and secondly the mineralogical changes under more or less extended hydromorphic conditions. The degree of evolution of ferralitic cover is also related to the hydrodynamic functioning and chemical properties of the soil. Geological substrate, topography and slope have also been taken into account. Analysis of the influence of environmental variables on plant cover has been performed using the Ecological Profiles method and Correspondence Analysis (CA) of the table of ecological profiles. The forest community seems to be dependent on the soil and the topographical features that govern it. There are significant, exclusive soil-species links for each soil functioning mapping unit. However, the highest proportion of significant positive links is connected with a thick micro-aggregate d horizon (25{\%}). Several species are of real value as indicators and more particularly enable differentiation between the forest stands of typical ferralitic soil and the ones of thinned out, transformed and hydromorphic soils. The CA of the species by environmental variables matrices reveals two significant factorial axes. The first can be associated with the drainage mainly related to the thinning of the soil and the second with the hydromorphic conditions related to the topography. The vegetation ordination of the stands ({\textless}?{\textgreater} 0.25 ha) delimited in the various soil domains clearly shows that changes in ferralitic cover and in particular the transition from soil with deep vertical drainage to soil with superficial lateral drainage is accompanied by substantial changes in the forest community.},
-author = {Sabatier, Daniel and Grimaldi, Michel and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise and Guillaume, Julie and Godron, Michel and Dosso, Mireille and Curmi, Pierre},
-journal = {Plant Ecology},
-keywords = {Sabatier (1997).pdf},
-mendeley-tags = {Sabatier (1997).pdf},
-number = {1},
-pages = {81--108},
-title = {{The influence of soil cover organization on the floristic and structural heterogeneity of a Guianan rain forest}},
-volume = {131},
-year = {1997}
-}
-@article{Balmford1996b,
-abstract = {R ecent analyses confirm that urgent attempts to catalogue the distribution of biological diversity may be facilitated by focusing at the level of genera or families rather than species. However, questions remain over the application of higher-taxon surveys to identify networks of priority areas for conservation action. Is the close spatial match between species and higher-taxon richness at global and regional scales reiterated when sites are locally distributed? How much money is saved by the higher-taxon approach? And how does using genus or family information affect the efficiency with which spatial priorities for conservation are identified? We examined these issues using data on the diversity of woody plants in Sri Lankan forests. We found that at this local scale, the family and particularly generic richness of sites was closely linked to their species richness, independently of variation in site size. Moreover, fieldwork in an additional forest showed that targeting woody plant genera and families rather than species reduced survey costs by a minimum of 60{\%} and 85{\%} respectively. Most importantly, while using family data in site-selection algorithms led to the loss from reserve networks of around 7-10{\%} of woody plant species, using genera rather than species had virtually no effect on the representation of species in priority sites. These results thus confirm that judicious use of the higher-taxon approach is indeed a valuable technique for improving the cost effectiveness of field surveys for local conservation planning in the tropics.},
-author = {Balmford, Andrew and Jayasuriya, A. H. M. and Green, M. J. B.},
-doi = {10.1098/rspb.1996.0230},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Balmford, Jayasuriya, Green - 1996 - Using higher-taxon richness as a surrogate for species richness II. Local applications.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-pages = {1571--1575},
-title = {{Using higher-taxon richness as a surrogate for species richness: II. Local applications}},
-url = {http://rspb.royalsocietypublishing.org/content/263/1376/1571.short},
-volume = {263},
-year = {1996}
-}
-@article{Haegeman2013,
-abstract = {Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ('Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Haegeman, Bart and Hamelin, J{\'{e}}r{\^{o}}me and Moriarty, John and Neal, Peter and Dushoff, Jonathan and Weitz, Joshua S},
-doi = {10.1038/ismej.2013.10},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haegeman et al. - 2013 - Robust estimation of microbial diversity in theory and in practice.pdf:pdf},
-journal = {The ISME journal},
-number = {6},
-pages = {1092--101},
-title = {{Robust estimation of microbial diversity in theory and in practice}},
-url = {http://dx.doi.org/10.1038/ismej.2013.10},
-volume = {7},
-year = {2013}
-}
-@book{Gatrell1983,
-address = {Oxford},
-author = {Gatrell, Antony C.},
-booktitle = {Contemporary Problems in Geography},
-isbn = {9780198741282},
-pages = {1--195},
-publisher = {Clarendon Press},
-title = {{Distance and Space: A Geographical Perspective}},
-year = {1983}
-}
-@article{Wurtz2008,
-abstract = {The species-area relationship is one of the central generalizations in ecology; however, its origin has remained a puzzle. Since ecosystems are understood as energy transduction systems, the regularities in species richness are considered to result from ubiquitous imperatives in energy transduction. From a thermodynamic point of view, organisms are transduction mechanisms that distribute an influx of energy down along the steepest gradients to the ecosystem's diverse repositories of chemical energy, that is, populations of species. Transduction machineries, that is, ecosystems assembled fromnumerous species,may emerge and evolve toward high efficiency on large areas that hold more matter than small ones. This results in thewell-known logistic-like relationship between the area and the number of species. The species-area relationship is understood, in terms of thermodynamics, to be the skewed cumulative curve of chemical energy distribution that is commonly known as the species-abundance relationship.},
-author = {W{\"{u}}rtz, Peter and Annila, Arto},
-doi = {10.1155/2008/654672},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/W{\"{u}}rtz, Annila - 2008 - Roots of Diversity Relations.pdf:pdf},
-journal = {Journal of Biophysics},
-pages = {Article ID 654672},
-title = {{Roots of Diversity Relations}},
-url = {http://dx.doi.org/10.1155/2008/654672},
-volume = {2008},
-year = {2008}
-}
-@article{Haase2001,
-abstract = {In dryland ecosystems and other harsh environments, a large part of the vegetation is often clustered, appearing as islands. If independent species, usually colonizers, can be distinguished from species which are dependent on the presence of the colonizing species for successful establishment and/or persistence, the type of spatial pattern of the association - isotropic (spatially symmetric) or anisotropic (spatially asymmetric) - can give information on the underlying environmental factors driving the process of association. Modified spatial pattern analysis based on Ripley's K-function can be applied to bivariate clustered patterns by cardinal direction in order to detect possible anisotropy in the pattern of association. The method was applied to mapped distribution patterns of two types of semiarid shrubland in southeastern Spain. In shrubland of Retama sphaerocarpa, low shrubs of Artemisia barrelieri were significantly clustered under the canopy of the Retama shrubs in all four cardinal directions, suggesting an isotropic facilitation effect. In low shrubland dominated by Anthyllis cytisoides and Artemisia barrelieri, Anthyllis shrubs occurred more frequently than expected on the eastern side (and downslope) of an Artemisia shrub. The possible environmental factors driving the two association patterns are discussed and recommendations for further applications of the analytical method are given.},
-author = {Haase, Peter},
-doi = {10.1111/j.1654-1103.2001.tb02623.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haase - 2001 - Can isotropy vs. anisotropy in the spatial association of plant species reveal physical vs. biotic facilitation.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {1},
-pages = {127--136},
-title = {{Can isotropy vs. anisotropy in the spatial association of plant species reveal physical vs. biotic facilitation?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2001.tb02623.x/abstract},
-volume = {12},
-year = {2001}
-}
-@article{Champely2002,
-abstract = {We study the complementary use of Rao's theory of diversity (1986) and Euclidean metrics. The first outcome is a Euclidean diversity coefficient. This index allows to measure the diversity in a set of species beyond their relative abundances using biological information about the dissimilarity between the species. It also involves geometrical interpretations and graphical representations. Moreover, several populations (e.g., different sites) can be compared using a Euclidean dissimilarity coefficient derived from the Euclidean diversity coefficient. These proposals are used to compare breeding bird communities living in comparable habitat gradients in different parts of the world.},
-author = {Champely, St{\'{e}}phane and Chessel, Daniel},
-doi = {10.1023/A:1015170104476},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Champely, Chessel - 2002 - Measuring biological diversity using Euclidean metrics.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {2},
-pages = {167--177},
-title = {{Measuring biological diversity using Euclidean metrics}},
-url = {http://link.springer.com/article/10.1023/A:1015170104476},
-volume = {9},
-year = {2002}
-}
-@article{Tsallis1994,
-author = {Tsallis, Constantino},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsallis - 1994 - What are the numbers that experiments provide.pdf:pdf},
-journal = {Qu{\'{i}}mica Nova},
-number = {6},
-pages = {468--471},
-title = {{What are the numbers that experiments provide?}},
-url = {http://quimicanova.sbq.org.br/detalhe{\_}artigo.asp?id=5517},
-volume = {17},
-year = {1994}
-}
-@article{Ogata1984,
-abstract = {The likelihood procedure for estimating the pairwise interaction potential function is developed for statistical analysis of homogeneous spatial point patterns. Approximation methods of the normalizing factor of Gibbs canonical distribution are discussed both to estimate a scale parameter and to measure the softness (or hardness) of repulsive interactions. The approximations are useful up to a considerably high density. The validity of our procedure is demonstrated by some computer experiments. Some real data are analysed.},
-author = {Ogata, Yosihiko and Tanemura, Masaharu},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ogata, Tanemura - 1984 - Likelihood Analysis of Spatial Point Patterns.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {3},
-pages = {496--518},
-title = {{Likelihood Analysis of Spatial Point Patterns}},
-url = {http://www.jstor.org/stable/2345690},
-volume = {46},
-year = {1984}
-}
-@article{Hardy2007,
-abstract = {1 Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2 Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. IST, PST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. FST, NST). 3 Two coefficients which express community differentiation among sites from species identity (IST) or species phylogeny (PST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (?ST) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4 We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (PST {\textgreater} IST or ?ST {\textgreater} 0) or phylogenetic overdispersion (PST {\textless} IST or ?ST {\textless} 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations. 5 IST, PST or ?ST can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears. 6 We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions. 7 The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species).},
-author = {Hardy, Olivier J. and Senterre, Bruno},
-doi = {10.1111/j.1365-2745.2007.01222.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hardy, Senterre - 2007 - Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {493--506},
-title = {{Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity}},
-url = {http://dx.doi.org/10.1111/j.1365-2745.2007.01222.x},
-volume = {95},
-year = {2007}
-}
-@article{Jayet1996,
-abstract = {Des travaux r{\'{e}}cents en th{\'{e}}orie de la localisation et en g{\'{e}}ographie {\'{e}}conomique sugg{\`{e}}rent qu'entreprises et m{\'{e}}nages ne deviennent pas indiff{\'{e}}rents {\`{a}} leur localisation lorsque les frais de transport baissent de mani{\`{e}}re importante. Cette baisse provoque un d{\'{e}}cloisonnement des march{\'{e}}s, favorable {\`{a}} l'accentuation de la concurrence, qui conduit les entreprises {\`{a}} reconstituer leur pouvoir de march{\'{e}} au travers de la diff{\'{e}}renciation de leurs produits. Les entreprises ne craignent plus la proximit{\'{e}} de concurrents et se regroupent en des emplacements accessibles {\`{a}} une client{\`{e}}le potentielle plus nombreuse. Les individus sont attir{\'{e}}s par les m{\'{e}}tropoles offrant une grande vari{\'{e}}t{\'{e}} de produits et une large gamme d'opportunit{\'{e}}s d'embauche. De ce fait, la polarisation est pour une bonne part la facette territoriale de la croissance {\'{e}}conomique. L'am{\'{e}}nagement du territoire ne doit donc pas {\`{a}} {\^{e}}tre con{\c{c}}u comme une politique cherchant {\`{a}} la contrecarrer. Am{\'{e}}nager le territoire, c'est plut{\^{o}}t trouver un {\'{e}}quilibre raisonnable entre les consid{\'{e}}rations d'{\'{e}}quit{\'{e}} dans la distribution g{\'{e}}ographique des activit{\'{e}}s et leurs co{\^{u}}ts en termes de croissance globale lorsqu'il y a conflit entre la r{\'{e}}partition spatiale des fruits de la croissance et son rythme d'{\'{e}}volution. Recent advances in location theory and economic geography suggest that firms and households do not become indifferent with respect to their locations when transport costs sharply fall. The intensification of competition leads firms to differentiate their products in order to reconstruct their profit margins. Firms no longer fear the proximity of their competitors and tend to agglomerate in central places where on average they are close to their potential customers. Similarly individuals are attracted by cities providing a wide array of products as well as a variety of specialized jobs. Hence polarization is to be viewed as the geographical counterpart of economic growth. Regional policy should therefore not stand against the process of polarization. Instead the objective is to find the appropriate balance between equity considerations in the spatial distribution of activities and the corresponding costs in terms of growth opportunities.},
-author = {Jayet, Hubert and Puig, Jean-Pierre and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jayet, Puig, Thisse - 1996 - Enjeux {\'{e}}conomiques de l'organisation du territoire.pdf:pdf},
-journal = {Revue d'{\'{e}}conomie politique},
-number = {1},
-pages = {127--158},
-title = {{Enjeux {\'{e}}conomiques de l'organisation du territoire}},
-url = {http://www.jstor.org/stable/24700543},
-volume = {106},
-year = {1996}
-}
-@article{Zimmerman2012,
-abstract = {A convincing body of evidence shows that as it is presently codified, sustainable forest-management (SFM) logging implemented at an industrial scale guarantees commercial and biological depletion of high-value timber species within three harvests in all three major tropical forest regions. The minimum technical standards necessary for approaching ecological sustainability directly contravene the prospects for financial profitability. Therefore, industrial-scale SFM is likely to lead to the degradation and devaluation of primary tropical forests as surely as widespread conventional unmanaged logging does today Recent studies also show that logging in the tropics, even using SFM techniques, releases significant carbon dioxide and that carbon stocks once stored in logged timber and slash takes decades to rebuild. These results beg for a reevaluation of the United Nations Framework Convention on Climate Change proposals to apply a Reducing Emissions from Deforestation and Forest Degradation subsidy for the widespread implementation of SFM logging in tropical forests. However, encouraging models of the successful sustainable management of tropical forests for timber and nontimber products exist at local-community scales.},
-annote = {ISI Document Delivery No.: 942EJ
-Times Cited: 0
-Cited Reference Count: 69
-Zimmerman, Barbara L. Kormos, Cyril F.
-Amer inst biological sci
-Washington},
-author = {Zimmerman, B. L. and Kormos, C. F.},
-doi = {10.1525/bio.2012.62.5.9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zimmerman, Kormos - 2012 - Prospects for Sustainable Logging in Tropical Forests.pdf:pdf},
-journal = {Bioscience},
-number = {5},
-pages = {479--487},
-title = {{Prospects for Sustainable Logging in Tropical Forests}},
-url = {http://bioscience.oxfordjournals.org/content/62/5/479},
-volume = {62},
-year = {2012}
-}
-@article{Stirling2001,
-abstract = {Diversity (or biodiversity) is typically measured by a species count (richness) and sometimes with an evenness index; it may also be measured by a proportional statistic that combines both measures (e.g., Shannon-Weiner index or H'). These diversity measures are hypothesized to be positively and strongly correlated, but this null hypothesis has not been tested empirically. We used the results of Caswell's neutral model to generate null relationships between richness (S), evenness (J'), and proportional diversity (H'). We tested predictions of the null model against empirical relationships describing data in a literature survey and in four individual studies conducted across various scales. Empirical relationships between log S or J' and H' differed from the null model when {\textless}10 species were tested and in plants, vertebrates, and fungi. The empirical relationships were similar to the null model when {\textgreater}10 and {\textless}100 species were tested and in invertebrates. If {\textgreater}100 species were used to estimate diversity, the relation between log S and H' was negative. The strongest predictive models included log S and J'. A path analysis indicated that log S and J' were always negatively related, that empirical observations could not be explained without including indirect effects, and that differences between the partials may indicate ecological effects, which suggests that S and J' act like diversity components or that diversity should be measured using a compound statistic.},
-author = {Stirling, Gray and Wilsey, Brian J.},
-doi = {10.1086/321317},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stirling, Wilsey - 2001 - Empirical Relationships between Species Richness, Evenness, and Proportional Diversity.pdf:pdf},
-journal = {The American naturalist},
-number = {3},
-pages = {286--299},
-title = {{Empirical Relationships between Species Richness, Evenness, and Proportional Diversity}},
-url = {http://www.journals.uchicago.edu/doi/pdfplus/10.1086/321317},
-volume = {158},
-year = {2001}
-}
-@article{Duranton2005,
-abstract = {To study the detailed location patterns of industries, and particularly the tendency for industries to cluster relative to overall manufacturing, we develop distance-based tests of localization. In contrast to previous studies, our approach allows us to assess the statistical significance of departures from randomness. In addition, we treat space as continuous instead of using an arbitrary collection of geographical units. This avoids problems relating to scale and borders. We apply these tests to an exhaustive U.K. data-set. For four-digit industries, we find that (i) 52{\%} of them are localized at a 5{\%} confidence level, (ii) localization mostly takes place at small scales below 50 km, (iii) the degree of localization is very skewed, and (iv) industries follow broad sectoral patterns with respect to localization. Depending on the industry, smaller establishments can be the main drivers of both localization and dispersion. Three-digit sectors show similar patterns of localization at small scales as well as a tendency to localize at medium scales.},
-author = {Duranton, Gilles and Overman, Henry G},
-doi = {10.1111/0034-6527.00362},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton, Overman - 2005 - Testing for Localisation Using Micro-Geographic Data.pdf:pdf},
-journal = {Review of Economic Studies},
-number = {4},
-pages = {1077--1106},
-title = {{Testing for Localisation Using Micro-Geographic Data}},
-url = {https://academic.oup.com/restud/article/72/4/1077/1583166/Testing-for-Localization-Using-Micro-Geographic},
-volume = {72},
-year = {2005}
-}
-@article{Bernstein1989,
-abstract = {In this paper we estimate a model of production and investment based on the theory of dynamic duality. We are particularly interested in the effects of R{\&}D spillovers and in calculating the social and private rates of return. There are three effects associated with the intra-industry R{\&}D spillover. First, costs decline as knowledge expands for the externality-receiving firms. Second, production structures are affected, as factor demands change in response to the spillover. Third, the rates of capital accumulation are affected by the R{\&}D spillover. These cost-reducing, factor-biasing and capital adjustment effects are estimated for four industries. The existence of R{\&}D spillovers implies that the social and private rates of return to R{\&}D capital differ. We estimate that the social return exceeds the private return in each industry. Moreover, there is significant variation across industries in the differential between the social and private rates of return.},
-author = {Bernstein, Jeffrey I. and Nadiri, M. Ishaq},
-doi = {10.2307/2297460},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bernstein, Nadiri - 1989 - Research and Development and Intra-industry Spillovers An Empirical Application of Dynamic Duality.pdf:pdf},
-journal = {The Review of Economic Studies},
-number = {2},
-pages = {249--267},
-title = {{Research and Development and Intra-industry Spillovers: An Empirical Application of Dynamic Duality}},
-url = {http://restud.oxfordjournals.org/content/56/2/249.short},
-volume = {56},
-year = {1989}
-}
-@article{Liu2006,
-abstract = {Diversity indices have been widely used in ecological research, but they remain problematic in that different indices may rank communities inconsis- tently. This problem can be solved by using diversity ordering methods, the output of which is a diversity profile in graphical form for each community being compared. In this paper, we demonstrate that existing diversity ordering methods can be classified into four groups and that within-group methods are essentially equivalent, while among-group methods are not. We find that the intrinsic diversity-related methods—i.e., the group containing the right tail-sum method, the logarithmic dominance plot, the majorization method, and the k-dominance plot—provide the most stringent test of diversity ordering, and we recommend the right tail-sum method as the method of preference for practical purposes.},
-author = {Liu, Canran and Whittaker, Robert J. and Ma, Keping and Malcolm, Jay R.},
-doi = {10.1007/s10144-006-0026-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liu et al. - 2006 - Unifying and distinguishing diversity ordering methods for comparing communities.pdf:pdf},
-journal = {Population Ecology},
-number = {2},
-pages = {89--100},
-title = {{Unifying and distinguishing diversity ordering methods for comparing communities}},
-url = {http://link.springer.com/10.1007/s10144-006-0026-0},
-volume = {49},
-year = {2006}
-}
-@article{Whittaker2001,
-abstract = {Aim Current weaknesses of diversity theory include: a failure to distinguish different biogeographical response variables under the general heading of diversity; and a general failure of ecological theory to deal adequately with geographical scale. Our aim is to articulate the case for a top-down approach to theory building, in which scale is addressed explicitly and in which different response variables are clearly distinguished. Location The article draws upon both theoretical contributions and empirical analyses from all latitudes, focusing on terrestrial ecosystems and with some bias towards (woody) plants. Methods We review current diversity theory and terminology in relation to scale of applicability. As a starting point in developing a general theory, we take the issue of geographical gradients in species richness as a main theme and evaluate the extent to which commonly cited theories are likely to operate at scales from the macro down to the local. Results A degree of confusion surrounds the use of the terms alpha, beta and gamma diversity, and the terms local, landscape and macro-scale are preferred here as a more intuitive framework. The distinction between inventory and differentiation diversity is highlighted as important as, in terms of scale of analysis, are the concepts of focus and extent. The importance of holding area constant in analysis is stressed, as is the notion that different environmental factors exhibit measurable heterogeneity at different scales. Evaluation of several of the most common diversity theories put forward for the grand clines in species richness, indicates that they can be collapsed to dynamic hypotheses based on climate or historical explanations. The importance of the many ecological/biological mechanisms that have been proposed is evident mainly at local scales of analysis, whilst at the macro-scale they are dependent largely upon climatic controls for their operation. Local communities have often been found not to be saturated, i.e. to be non-equilibrial. This is argued, perhaps counter-intuitively, to be entirely compatible with the persistence through time of macro-scale patterns of richness that are climatically determined. The review also incorporates recent developments in macroecology, Rapoport's rule, trade-offs, and the importance of isolation, landscape impedance and geometric constraints on richness (the mid-domain effect) in generating richness patterns; highlighting those phenomena that are contributory to the first-order climatic pattern, and those, such as the geometric constraints, that may confound or obscure these patterns. Main conclusions A general theory of diversity must necessarily cover many disparate phenomena, at various scales of analysis, and cannot therefore be expressed in a simple formula, but individual elements of this general theory may be. In particular, it appears possible to capture in a dynamic climate-based model and 'capacity rule', the form of the grand cline in richness of woody plants at the macro-scale. This provides a starting point for a top-down, global-to-local, macro-to-micro scale approach to modelling richness variations in a variety of taxa. Patterns in differentiation/endemicity, on the other hand, require more immediate attention to historical events, and to features of geography such as isolation. Thus, whilst we argue that there are basic physical principles and laws underlying certain diversity phenomena (e.g. macro-scale richness gradients), a pluralistic body of theory is required that incorporates dynamic and historical explanation, and which bridges equilibrial and nonequilibrial concepts and ideas.},
-author = {Whittaker, Robert J. and Willis, Katherine J. and Field, Richard},
-doi = {10.1046/j.1365-2699.2001.00563.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker, Willis, Field - 2001 - Scale and species richness towards a general, hierarchical theory of species diversity.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {4},
-pages = {453--470},
-title = {{Scale and species richness: towards a general, hierarchical theory of species diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2699.2001.00563.x/abstract},
-volume = {28},
-year = {2001}
-}
-@article{Nanami1999,
-abstract = {1 Spatial patterns of two codominant dioecious tree species, Podocarpus nagi and Neolitsea aciculata, were analysed a t Mt . Mikasa, Nara City, Japan. Podocarpus nagi has a higher shade tolerance but a narrower seed dispersal range than Neolitsea aciculata. We examined the effects of dioecy on regeneration and coexistence of the two species. 2 Seeds of Podocarpus nagi are dispersed by gravity around female trees. Young plants of Podocarpus nagi were clumped and showed significant attraction to large female trees and significant repulsion from large inale trees. Dioecy therefore affected the spatial heterogeneity of plant density in the Podocarpus nagi population. 3 Seeds of Neolitsea aciculata are widely dispersed by birds, and young plants of Neolitsea aciculata therefore showed no significant attraction to female trees. This wide dispersal of seeds moderated the effects of dioecy on the spatial pattern in Neolitsea aciculata. 4 Large Neolitsea aciculata trees were clumped and showed significant attraction to large male Podocarpus nagi trees, suggesting that growth of Neolitsea aciculata is facilitated where young Podocarpus nagi plants are uncomon and competition is therefore less intense. 5 One effect of dioecy may be to produce a population structure for Podocarpus nagi that promotes its coexistence with Neolitsea aciculata.},
-author = {Nanami, Satoshi and Kawaguchi, Hideyuki and Yamakura, Takuo},
-doi = {10.1046/j.1365-2745.1999.00392.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nanami, Kawaguchi, Yamakura - 1999 - Dioecy-Induced Spatial Patterns of Two Codominant Tree Species, Podocarpus nagi and Neolitsea acicu.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {678--687},
-title = {{Dioecy-Induced Spatial Patterns of Two Codominant Tree Species, Podocarpus nagi and Neolitsea aciculata}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2745.1999.00392.x/full},
-volume = {87},
-year = {1999}
-}
-@article{Moles2005a,
-abstract = {Improved phylogenies and the accumulation of broad comparative data sets have opened the way for phylogenetic analyses to trace trait evolution in major groups of organisms. We arrayed seed mass data for 12,987 species on the seed plant phylogeny and show the history of seed size from the emergence of the angiosperms through to the present day. The largest single contributor to the present-day spread of seed mass was the divergence between angiosperms and gymnosperms, whereas the widest divergence was between Celastraceae and Parnassiaceae. Wide divergences in seed size were more often associated with divergences in growth form than with divergences in dispersal syndrome or latitude. Cross-species studies and evolutionary theory are consistent with this evidence that growth form and seed size evolve in a coordinated manner.},
-author = {Moles, Angela T. and Ackerly, David D. and Webb, Campbell O. and Tweddle, J. C. and Dickie, J. B. and Westoby, Mark},
-doi = {10.1126/science.1104863},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moles et al. - 2005 - A brief history of seed size.pdf:pdf},
-journal = {Science},
-number = {5709},
-pages = {576--580},
-title = {{A brief history of seed size}},
-volume = {307},
-year = {2005}
-}
-@article{Webb2006,
-author = {Webb, Campbell O. and Losos, Jonathan B. and Agrawal, Anurag A.},
-doi = {10.1890/0012-9658(2006)87[1:IPICE]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Webb, Losos, Agrawal - 2006 - Integrating Phylogenies into Community Ecology.pdf:pdf},
-journal = {Ecology},
-number = {sp7},
-pages = {S1--S2},
-title = {{Integrating Phylogenies into Community Ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282006{\%}2987[1:IPICE]2.0.CO{\%}3B2/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Beguinot2015a,
-abstract = {Incomplete species samplings are deemed to remain the common practice in those groups of animals, such as small or micro- invertebrates, with numerous species that often are more or less difficult to detect in the field. Thus, extrapolating the Species Accumulation Curve as far as possible beyond the actual sample size may thus serve as a useful (although imperfect) surrogate to the desired, but practically inaccessible, complete samplings. In this context, several kinds of theoretical or empirical models for the Species Accumulation Curve and also a lot of estimators of the asymptotic limit of the Curve (i.e. total species richness) have been proposed. The practical issue is now to select appropriately among these numerous, different propositions. Here, I show that realistic Species Accumulation Curves are constrained to respect a general mathematical relationship, which, in turn, may serve to discriminate and select among the available models of Species Accumulation Curves and, as well, among the different formulations of the estimators of species richness that are commonly referred to.As a result of the application of this screening approach, it follows that, for the generality of cases (i.e. ratio singletons/doubletons larger than 0.6), a specific formulation of the Species Accumulation Curve (bi-hyperbolic with exponents -1 and -2 for sample size) complies at best. Accordingly, the more appropriate estimator of total species richness is Jackknife-2. Only when the ratio singletons/doubletons happens to fall beneath 0.6, Chao estimator may then be preferred. This is the case when samplings closely approach exhaustivity or when they address assemblages with unusually homogeneous abundances of species.},
-author = {B{\'{e}}guinot, Jean},
-doi = {10.9734/ARRB/2015/22351},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/B{\'{e}}guinot - 2015 - Extrapolation of the Species Accumulation Curve for Incomplete Species Samplings A New Nonparametric Approach to Estim.pdf:pdf},
-journal = {Annual Research {\&} Review in Biology},
-number = {5},
-pages = {1--9},
-title = {{Extrapolation of the Species Accumulation Curve for Incomplete Species Samplings: A New Nonparametric Approach to Estimate the Degree of Sample Completeness and Decide when to Stop Sampling}},
-url = {http://sciencedomain.org/abstract/12125},
-volume = {8},
-year = {2015}
-}
-@book{Pernes1984,
-address = {Paris},
-editor = {Pern{\`{e}}s, J.},
-isbn = {92-9028-043-3},
-publisher = {Agence de Coop{\'{e}}ration culturelle et technique},
-title = {{Gestion des ressources g{\'{e}}n{\'{e}}tiques des plantes. Tome 2 : Manuel}},
-year = {1984}
-}
-@article{Laurance1998,
-author = {Laurance, William F. and Ferreira, Leandro V. and Rankin-de-Merona, Judy M. and Hutchings, Roger W.},
-doi = {10.1111/j.1744-7429.1998.tb00106.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Laurance et al. - 1998 - Influence of Plot Shape on Estimates of Tree Diversity and Community Composition in Central Amazonia.pdf:pdf},
-journal = {Biotropica},
-number = {4},
-pages = {662--665},
-title = {{Influence of Plot Shape on Estimates of Tree Diversity and Community Composition in Central Amazonia}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7429.1998.tb00106.x/abstract},
-volume = {30},
-year = {1998}
-}
-@phdthesis{Forget1988,
-author = {Forget, Pierre-Michel},
-publisher = {Universit{\'{e}} de Paris VI},
-title = {{Diss{\'{e}}mination et r{\'{e}}g{\'{e}}n{\'{e}}ration naturelle de huit esp{\`{e}}ces d'arbres en for{\^{e}}t guyanaise}},
-year = {1988}
-}
-@article{DeBello2017,
-abstract = {Functional traits and phylogeny offer different, and often complementary, information about ecological differences between species, an essential step to uncover biodiversity assembly mechanisms and their feedbacks to ecosystem functions. However, traits and phylogeny are often related due to underlying trait evolution. Consequently, when combined, their shared information can be overemphasized, hindering their complementarity. It is therefore desirable to decouple their unique and overlapping contributions. We propose a conceptual and mathematical framework that produces a set of meaningful measures of ecological differences between species. We test the properties of these measures and the validity of the approach with extensive simulated data to show (i) the information provided by decoupling traits from phylogeny and vice versa, and (ii) that decoupling trait and phylogenetic information can uncover otherwise hidden signals underlying species coexistence and turnover. The application of the approach is further illustrated using a large dataset of Central European meadows as a case study. Decoupling traits and phylogeny particularly reveals the importance of differentiation between phylogenetically related species, which can be essential to understand species replacements along environmental gradients and the combined action of environmental filtering and limiting similarity within communities. Decoupling traits and phylogeny provides an avenue for connecting macro-evolutionary and local factors affecting coexistence and for understanding how complex species differences affect multiple ecosystem functions. We present an R function called ‘decouple', which allows a simple and wide application of the framework.},
-author = {de Bello, Francesco and {\v{S}}milauer, Petr and Diniz-Filho, Jose Alexandre F. and Carmona, Carlos Perez and Lososov{\'{a}}, Zdeňka and Herben, Tom{\'{a}}{\v{s}} and G{\"{o}}tzenberger, Lars},
-doi = {10.1111/2041-210X.12735},
-editor = {M{\"{u}}nkem{\"{u}}ller, Tamara},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Bello et al. - 2017 - Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-month = {oct},
-number = {10},
-pages = {1200--1211},
-title = {{Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12735/abstract},
-volume = {8},
-year = {2017}
-}
-@incollection{Arbia2010a,
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego},
-booktitle = {Handbook of Research Methods and Applications in Economic Geography},
-chapter = {6},
-editor = {Karlsson, Charlie and Andersson, Martin and Norman, Therese},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia, Espa, Giuliani - 2015 - Analysis of spatial concentration and dispersion.pdf:pdf},
-isbn = {9780857932662},
-pages = {135--157},
-publisher = {Edward Elgar Publishing},
-title = {{Analysis of spatial concentration and dispersion}},
-year = {2015}
-}
-@article{Prance1996,
-author = {Prance, G T},
-journal = {Philosophical Transactions of the Royal Society of London Series},
-pages = {823--33},
-title = {{Islands in Amazonia}},
-volume = {B 351},
-year = {1996}
-}
-@article{Swap1992,
-abstract = {Copied as is: Saharan dust is shown to enter the Central Amazon Basin (CAB) in bursts which accompany major wet season rain systems. Low-level horizontal convergence feeding these rain systems draws dust from plumes which have crossed the tropical Atlantic under the large-scale circulation fields. Mass exchange of air between the surface and 4 km over the eastern Amazon basin is calcualted using rawinsonde data collected during storm events. Mean concentrations of dust observed by aircraft over the western tropical Atlantic are used to calculate the amount of dust injected into the Basin. Individual storm events inject some 480,000 tons of dust into the northeastern Amazon Basin. Storm and dust climatology suggest that the annual importation of dust is in the order of 13Mtons. In the northeastern basin, this may amount to as much as 190 kg ha-1 yr-1. Deposition of trace species, such as phosphate, associated with this dust ranges from 1-4 kg ha-1 yr-1. Uncertainties in these estimates are not believed to be greater than ±50{\%} and may as low as ±20{\%}. The deposition fluxes from Saharan dust are essentially identical to the CAB wet deposition fluxes from precipitation in the wet season; a result that implies that the major ionic composition of rain water in the CAB wet season may be strongly influenced by inputs of material originating on the African continent nearly 5000 km away. The total amount of Saharan dust calculated to enter the Amazon basin is 1/2 to 1/3 of that estimated to cross 60°W longitude between 10° and 25°N latitude. We conclude that part of the productivity of the Amazon rain forest is dependent upon critical trace elements contained in the soil dust originating in the Sahara/Sahel. This dependence should be reflected by expansions and contractions of the Amazon rain forst in direct relationship to expansions and contractions of the Sahara/Sahel. Turnover rates for nutrient species deposited with Saharan dust in the Amazon Basin suggest a time scale of 500 to 20,000 years. We believe the dependence of one large ecosystem upon another separated by an ocean and coupled by the atmosphere to be fundamentally important to any view of how the global system functions. Any strategy designed to preserve the Amazonian rain forest or any part thereof should equally concern itself with the inter-relationship between the rain forest, global climate and arid zones well removed from Amazonia. --{\textgreater} not all rains in NE South America are associated with dust, but all dust events are associated with rains.},
-author = {Swap, R and Garstang, M and Greco, S and Talbot, R and K{\aa}llberg, P},
-doi = {10.1034/j.1600-0889.1992.t01-1-00005.x},
-journal = {Tellus},
-number = {2},
-pages = {133--149},
-title = {{Saharan dust in the Amazon Basin}},
-volume = {44B},
-year = {1992}
-}
-@incollection{Catin1994a,
-address = {Paris},
-author = {Catin, Maurice},
-booktitle = {Encyclop{\'{e}}die d'Economie Spatiale},
-editor = {Audray, Jean-Paul and Bailly, Antoine and Derycke, Pierre-Henri and Huriot, Jean-Marie},
-pages = {105--109},
-publisher = {Economica},
-title = {{Economies d'agglom{\'{e}}ration}},
-volume = {Chapitre 1},
-year = {1994}
-}
-@article{Bacaro2013a,
-abstract = {A simple analytical procedure to test for differences in beta diversity among sets of plots has been recently presented. Here, we describe an improved ran- domization procedure that replaces the one previously proposed. This procedure consists of shuffling within- group dissimilarities among groups and disregarding between-group dissimilarities. By repeating this opera- tion many times, a distribution of the test statistics under the null hypothesis of no differences in the mean plot-to- plot dissimilarities within groups is obtained. This pro- cedure ensures that the correct null model is selected. To describe this new procedure, we used plant and water beetle (Coleoptera) data collected from 45 permanent ponds. Beta diversity was compared between plant and water beetle (Coleoptera) assemblages.},
-annote = {Test de la diversit{\'{e}} b{\^{e}}ta entre communaut{\'{e}}s. Beta est pris comme une variable quelconque et la statistique F d'une Anova est calcul{\'{e}}e.
-Pour conna{\^{i}}tre sa significativit{\'{e}}, les valeurs sont permut{\'{e}}es entre communaut{\'{e}}s et le quantile de F est la p-value du test.},
-author = {Bacaro, Giovanni and Gioria, Margherita and Ricotta, Carlo},
-doi = {10.1007/s11284-013-1043-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro, Gioria, Ricotta - 2013 - Beta diversity reconsidered.pdf:pdf},
-journal = {Ecological Research},
-number = {3},
-pages = {537--540},
-title = {{Beta diversity reconsidered}},
-url = {http://link.springer.com/10.1007/s11284-013-1043-z},
-volume = {28},
-year = {2013}
-}
-@unpublished{Feser2001a,
-abstract = {Most studies of industry clusters in states and regions define clusters as localized concentrations of linked sectors and enterprises along with supporting non-business organizations and programs. The challenge for researchers and development practitioners undertaking such studies is to find a means of systematically identifying clusters given typical sub-state industry data and virtually no information on direct patterns of interaction between regional firms. Ideally, cluster studies should also acknowledge development opportunities afforded by clusters in neighboring states or border regions, further complicating the analysis. In this paper, we argue that a hybrid methodology that combines an aspatial analysis of interindustry linkages with spatial statistical analysis of employment patterns can yield rich information about industry clusters in state and sub-state areas. We illustrate the approach in a study of Kentucky's economy.},
-author = {Feser, Edward J. and Koo, J. and Renski, H. and Sweeney, Stuart H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser et al. - 2001 - Incorporating spatial analysis in applied industry cluster studies.pdf:pdf},
-title = {{Incorporating spatial analysis in applied industry cluster studies}},
-url = {http://www.planning.unc.edu/facstaff/faculty/feserDocs.htm},
-year = {2001}
-}
-@article{Faith2008,
-abstract = {New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst-case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species. Probabilistic PD provides a framework for single-species assessment that is well-integrated with a broader measurement of impacts on PD owing to climate change and other factors.},
-author = {Faith, Daniel P.},
-doi = {10.1111/j.1523-1739.2008.01068.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faith - 2008 - Threatened species and the potential loss of phylogenetic diversity conservation scenarios based on estimated extinction.pdf:pdf},
-journal = {Conservation Biology},
-number = {6},
-pages = {1461--70},
-title = {{Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/18798854},
-volume = {22},
-year = {2008}
-}
-@article{Inouye2005,
-author = {Inouye, Brian D.},
-doi = {10.1890/03-3180},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {262--265},
-title = {{The importance of the variance around the mean effect size of ecological processes: Comment}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/03-3180/abstract},
-volume = {86},
-year = {2005}
-}
-@article{Parmentier2014,
-abstract = {In highly diverse ecosystems, such as tropical forests, the relative importance of mechanisms underlying species coexistence (e.g. habitat filtering, competitive exclusion, neutral dynamics) is still poorly known and probably varies depending on spatial and phylogenetic scales. Here, we develop new approaches for dissecting simultaneously the phylogenetic structure of communities at different phylogenetic depths and spatial scales. We tested with simulations that our method is able to disentangle overdispersion and clustering effects occurring at contrasted phylogenetic depths. We applied our approaches to a 50 ha Forest Dynamic Plot located in Korup National Park (Cameroon) where 329,000 tree stems ≥ 1 cm in diameter were identified and mapped, and using a newly generated dated molecular phylogenetic tree based on 2 plastid loci (rbcL and matK), including 272 species from Korup (97{\%} of the individuals). Significant patterns of phylogenetic turnover were detected across 20x20m2 quadrats at most spatial scales, with higher turnover between topographic habitats than within habitats, indicating the prevalence of habitat filtering processes. Spatial phylogenetic clustering was detected over the entire range of phylogenetic depths indicating that competitive exclusion does not generate a pattern of phylogenetic overdispersion at this scale, even at a shallow phylogenetic depth. Using an individual-based approach, we also show that closely related species tended to aggregate spatially until a scale of 1 m. However, the signal vanishes at smaller distance, suggesting that competitive exclusion can balance the impact of environmental filtering at a very fine spatial scale. Synthesis Using new methods to characterize the structure of communities across spatial and phylogenetic scales, we inferred the relative importance of the mechanisms underlying species coexistence in tropical forests. Our analysis confirms that environmental filtering processes are key in the structuring of natural communities at most spatial scales. Although negative-density tends to limit coexistence of closely related species at very short distance ({\textless}1m), its influence is largely veiled by environmental filtering at larger distances. This article is protected by copyright. All rights reserved.},
-author = {Parmentier, Ingrid and R{\'{e}}jou-M{\'{e}}chain, Maxime and Chave, J{\'{e}}r{\^{o}}me and Vleminckx, Jason and Thomas, Duncan W. and Kenfack, David and Chuyong, George B. and Hardy, Olivier J.},
-doi = {10.1111/1365-2745.12254},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Parmentier et al. - 2014 - Prevalence of phylogenetic clustering at multiple scales in an African rain forest tree community.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {1008--1016},
-title = {{Prevalence of phylogenetic clustering at multiple scales in an African rain forest tree community}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12254/abstract},
-volume = {102},
-year = {2014}
-}
-@article{Gourlet-Fleury2005,
-abstract = {A major challenge for forest managers is to define the optimal cutting cycle to ensure that the resource is sustained in the long term. Matrix models of forest dynamics allow time-projection of diameter-class distributions and thus assessment of the time needed, after logging, to recover a given part of the exploitable stock. They are easy to build and they only require, as input variables, the diameter structure of the population(s) under scope. However, such models are based on a coarse description of tree population dynamics and must be used with caution. In particular, as trees are only described from a diameter threshold (usually 10 cm dbh), recruitment of a new tree cannot be linked with the preceding generation since too much time elapsed between seed dispersal and the installation of a 10-cm recruit. This causes predictions of matrix models to be highly questionable in the long term when ingrowth to larger dbh classes greatly depends on the way recruitment has been modelled. We used a case study from French Guiana to test whether or not a simple matrix model is reliable enough to help forest managers choose between management alternatives. We focused on the major timber species Dicorynia guianensis Amshoff (Caesalpiniaceae) harvested under a selective cutting regime. We compared predictions of D. guianensis stock recovery in the short and long term provided by two models: StoMat, a non-regulated matrix model, and SELVA, a single-tree distance dependent model explicitly simulating the entire species life cycle. Both models were independently calibrated on data from Paracou permanent sample plots. We showed that: (i) the short-term recovery of the exploitable stock predicted by StoMat is reliable for a large range of disturbance conditions; (ii) recruitment implementation in StoMat does not influence projections until the third felling cycle; (iii) for shared initial stand conditions SELVA and StoMat give consistent mid- and long-term predictions: the simple recruitment model used into StoMat could efficiently summarise the regeneration processes of the species under low felling intensity. Our results indicate that the current felling regime used in French Guiana may not be sustainable on a long-term basis. In any case, no more than 60{\%} of the initial stock would be recovered after logging. We conclude that simple models can provide as reliable predictions as more complicated ones. They may be sufficient to assess the recovery of a species' exploitable stock even in the long term, or at least assess the (un)sustainability of particular harvesting regimes.},
-author = {Gourlet-Fleury, Sylvie and Comu, Guillaume and Jesel, S{\'{e}}bastien and Dessard, H{\'{e}}l{\`{e}}ne and Jourget, Jean-Ga{\"{e}}l and Blanc, Lilian and Picard, Nicolas},
-doi = {10.1016/j.foreco.2005.01.010},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gourlet-Fleury et al. - 2005 - Using models to predict recovery and assess tree species vulnerability in logged tropical forests A case.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-2},
-pages = {69--86},
-title = {{Using models to predict recovery and assess tree species vulnerability in logged tropical forests: A case study from French Guiana}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112705000149},
-volume = {209},
-year = {2005}
-}
-@article{Feldpausch2011,
-abstract = {Tropical tree height-diameter (H:D) relationships may vary by forest type and region making large-scale es- timates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by cli- mate and/or forest structural characteristics (e.g. stand- level basal area, A). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass.},
-annote = {BG},
-author = {Feldpausch, Ted R. and Banin, L. and Phillips, Oliver L. and Baker, Timothy R. and Lewis, Simon L. and Quesada, Carlos A. and Affum-Baffoe, K. and Arets, Eric J. M. M. and Berry, N. J. and Bird, M. and Brondizio, E. S. and de Camargo, P. and Chave, J{\'{e}}r{\^{o}}me and Djagbletey, G. and Domingues, T. F. and Drescher, M. and Fearnside, P. M. and Fran{\c{c}}a, M. B. and Fyllas, N. M. and Lopez-Gonzalez, G. and Hladik, A. and Higuchi, N. and Hunter, M. O. and Iida, Y. and Salim, K. A. and Kassim, A. R. and Keller, M. and Kemp, J. and King, D. A. and Lovett, J. C. and Marimon, Beatriz Schwantes and Marimon-Junior, Ben Hur and Lenza, E. and Marshall, A. R. and Metcalfe, Daniel J. and Mitchard, E. T. A. and Moran, E. F. and Nelson, B. W. and Nilus, R. and Nogueira, E. M. and Palace, M. and Pati{\~{n}}o, Sandra and Peh, K. S. H. and Raventos, M. T. and Reitsma, J. M. and Saiz, G. and Schrodt, F. and Sonk{\'{e}}, B. and Taedoumg, H. E. and Tan, S. and White, L. and W{\"{o}}ll, Hannsjoerg and Lloyd, J.},
-doi = {10.5194/bg-8-1081-2011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feldpausch et al. - 2011 - Height-diameter allometry of tropical forest trees.pdf:pdf},
-journal = {Biogeosciences},
-number = {5},
-pages = {1081--1106},
-title = {{Height-diameter allometry of tropical forest trees}},
-url = {http://www.biogeosciences.net/8/1081/2011/},
-volume = {8},
-year = {2011}
-}
-@article{Houdebine1999,
-author = {Houdebine, Michel},
-journal = {Economie et Statistique},
-number = {6-7},
-pages = {189--204},
-title = {{Concentration G{\'{e}}ographique des Activit{\'{e}}s et Sp{\'{e}}cialisation des D{\'{e}}partements Fran{\c{c}}ais}},
-volume = {326-327},
-year = {1999}
-}
-@article{Ripley1976b,
-abstract = {The foundations of point process theory are surveyed. An abstract theory motivated by applications in stochastic geometry is presented. It is shown that it is sufficient to know only which sets are measurable and which are bounded in the basic space, where we use countability hypotheses rather than topological assumptions. (The sole exception is in the construction of probabilities where pseudo-topological hypotheses are needed.) It is shown that there are close connections with the random set theories of Kendall and Matheron.},
-author = {Ripley, Brian D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1976 - Locally Finite Random Sets Foundations for Point Process Theory.pdf:pdf},
-journal = {Annals of Probability},
-number = {6},
-pages = {983--994},
-title = {{Locally Finite Random Sets: Foundations for Point Process Theory}},
-url = {https://www.jstor.org/stable/2242957},
-volume = {4},
-year = {1976}
-}
-@article{VanLieshout1996,
-abstract = {The strength and range of interpoint interactions in a spatial point process can be quantified by the function J = (1 - G)/(1 - F), where G is the nearest-neighbour distance distribution function and F the empty space function of the process. J(r) is identically equal to 1 for a Poisson process; values of J(r) smaller or larger than 1 indicate clustering or regularity, respectively. We show that, for a large class of point processes, J(r) is constant for distances r greater than the range of spatial interaction. Hence both the range and type of interaction can be inferred from J without parametric model assumptions. It is also possible to evaluate J(r) explicitly for many point process models, so that J is also useful for parameter estimation. Various properties are derived, including the fact that the J function of the superposition of independent point processes is a weighted mean of the J functions of the individual processes. Estimators of J can be constructed from standard estimators of F and G. We compute estimates of J for several standard point pattern datasets and implement a Monte Carlo test for complete spatial randomness.},
-author = {{Van Lieshout}, M. N. M. and Baddeley, Adrian J.},
-doi = {10.1111/j.1467-9574.1996.tb01501.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Van Lieshout, Baddeley - 1996 - A nonparametric measure of spatial interaction in point patterns.pdf:pdf},
-journal = {Statistica Neerlandica},
-number = {3},
-pages = {344--361},
-title = {{A nonparametric measure of spatial interaction in point patterns}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9574.1996.tb01501.x/abstract},
-volume = {50},
-year = {1996}
-}
-@article{Mucchielli2003,
-abstract = {Les multinationales fran{\c{c}}aises, apr{\`{e}}s un d{\'{e}}but tardif dans leur processus d'internationalisation, r{\'{e}}alisent encore leurs investissements directs en Europe de fa{\c{c}}on fortement concentr{\'{e}}e. En 2000, plus de 38 {\%} des filiales fran{\c{c}}aises {\`{a}} l'{\'{e}}tranger sont localis{\'{e}}es dans l'Union europ{\'{e}}enne. Elles sont principalement implant{\'{e}}es dans les pays limitrophes (Royaume-Uni, Belgique, Allemagne, Italie, Espagne). Dans le pays d'accueil, ces investisseurs privil{\'{e}}gient essentiellement la r{\'{e}}gion de la capitale et les r{\'{e}}gions les plus industrialis{\'{e}}es. On analyse ici les d{\'{e}}terminants de la localisation des entreprises multinationales fran{\c{c}}aises dans sept pays europ{\'{e}}ens et dans quarante sept r{\'{e}}gions europ{\'{e}}ennes entre 1987 et 1994 dans l'industrie manufacturi{\`{e}}re, en s'appuyant sur l'examen de 614 d{\'{e}}cisions individuelles de localisation. L'{\'{e}}tude {\'{e}}conom{\'{e}}trique utilise un mod{\`{e}}le de logit imbriqu{\'{e}}. Il se fonde sur l'hypoth{\`{e}}se d'une structure hi{\'{e}}rarchique du processus d{\'{e}}cisionnel de localisation des entreprises en deux niveaux : les nations et les r{\'{e}}gions. Les r{\'{e}}sultats empiriques montrent que, sur la p{\'{e}}riode {\'{e}}tudi{\'{e}}e, la probabilit{\'{e}} d'implanter une filiale quelque part en Europe, d{\'{e}}pend {\`{a}} la fois de variables nationales et r{\'{e}}gionales. G{\'{e}}n{\'{e}}ralement, les d{\'{e}}terminants du choix de localisation n'influent qu'{\`{a}} un seul niveau g{\'{e}}ographique. Ainsi, pour l'implantation de filiales de multinationales fran{\c{c}}aises, les pays h{\^{o}}tes sont encore fortement diff{\'{e}}renci{\'{e}}s par leurs niveaux de salaires et les r{\'{e}}gions par des effets d'agglom{\'{e}}ration et de potentiel marchand. Par ailleurs, les effets d'agglom{\'{e}}ration, d{\'{e}}montr{\'{e}}s une fois de plus ici, permettent de valider la pertinence de politiques d'attractivit{\'{e}} bas{\'{e}}es sur l'existence ou le renforcement de p{\^{o}}les r{\'{e}}gionaux intra-industriels.},
-author = {Mucchielli, Jean-Louis and Puech, Florence},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mucchielli, Puech - 2003 - Internationalisation et localisation des firmes multinationales l'exemple des entreprises fran{\c{c}}aises en Euro.pdf:pdf},
-journal = {Economie et Statistique},
-keywords = {Mucchielli (2003).pd},
-mendeley-tags = {Mucchielli (2003).pd},
-pages = {129--144},
-title = {{Internationalisation et localisation des firmes multinationales : l'exemple des entreprises fran{\c{c}}aises en Europe}},
-volume = {363-365},
-year = {2003}
-}
-@article{Boutet2003,
-abstract = {Existing spatial patterns of a forest are in part a product of its disturbance history. Using laser altimetry and field measures of canopy top height to represent pre- and post-hurricane canopy topography, respectively, we measured changes in spatial patterns of stand structure of a United States southern mixed coniferous-deciduous forest. Autocorrelative and fractal properties were measured in this opportunistic study to quantify changes in canopy architecture along twelve, 190-250 m transects that were subjected to moderate to high levels of wind disturbance. Prior to the hurricane, canopy heights were autocorrelated at scales {\textless} 40 m with an average fractal dimension of 1.71. After the disturbance, autocorrelation disappeared; the average fractal dimension rose to 1.94. This shift towards spatial randomness illustrates part of the cyclical nature of ecosystem development. It shows how a catastrophic collapse of biomass accumulation corresponds to a decrease in ecosystem organization across a landscape.},
-author = {Boutet, Jeffry C. and Weishampel, John F.},
-doi = {10.1023/A:1026058312853},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Boutet, Weishampel - 2003 - Spatial pattern analysis of pre- and post-hurricane forest canopy structure in North Carolina, USA.pdf:pdf},
-journal = {Landscape Ecology},
-number = {6},
-pages = {553--559},
-title = {{Spatial pattern analysis of pre- and post-hurricane forest canopy structure in North Carolina, USA}},
-url = {http://link.springer.com/article/10.1023{\%}2FA{\%}3A1026058312853},
-volume = {18},
-year = {2003}
-}
-@article{Berger1970,
-abstract = {The diversity of a planktonic foraminiferal assemblage on the ocean floor depends on the state of preservation of that assemblage. As dissolution progresses, species diversity (number of species in the assemblage) decreases, but compound diversity (based on relative species abundance) first increases and then decreases; species dominance first decreases and then increases. The reason for these changes is that the species most susceptible to solution deliver moresediment to the ocean floor than do species with solution-resistant shells, possibly because the more soluble tests are produced in surface waters, where growth and production are greatest},
-author = {Berger, Wolfgang H. and Parker, Frances L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Berger, Parker - 1970 - Diversity of planktonic foraminifera in deep-sea sediments.pdf:pdf},
-journal = {Science},
-number = {3937},
-pages = {1345--1347},
-title = {{Diversity of planktonic foraminifera in deep-sea sediments}},
-volume = {168},
-year = {1970}
-}
-@article{Culhane2014,
-abstract = {Reliable ecosystem quality assessment of marine environments is increasingly important due to mounting pressures attributable to human activities. Biotic indices are widely used in studies to describe communities and indicate the ecological state of systems. This study focuses on benthic macroinvertebrate-based biotic indices for the assessment of ecosystem health. Indices used in ecosystem health assessment in the marine environment have mainly focussed on measuring structural components of the system while more recently the measurement of functional components has been highlighted. In this study the performance of traditional diversity indices based on structural components of benthic macroinvertebrate communities, indices developed for the EU Water Framework Directive, and indices which are based on functional biological traits of species were compared. The results indicated that while functional indices may provide a more detailed assessment of the benthic communities than structural indices, the overall outcome is broadly similar for both types of indices. This suggests measurement of functional indices may be unnecessary for routine monitoring purposes, although they may have value in revealing more specific aspects of change in a system. ?? 2014 Elsevier Ltd.},
-author = {Culhane, Fiona E. and Briers, Robert A. and Tett, Paul and Fernandes, Teresa F.},
-doi = {10.1016/j.ecolind.2014.03.009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Culhane et al. - 2014 - Structural and functional indices show similar performance in marine ecosystem quality assessment.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {271--280},
-title = {{Structural and functional indices show similar performance in marine ecosystem quality assessment}},
-url = {http://dx.doi.org/10.1016/j.ecolind.2014.03.009},
-volume = {43},
-year = {2014}
-}
-@article{Guisande2017,
-abstract = {There is no single diversity index that adequately summarises species diversity, since this is a multidimensional concept and hence should be quantified using a compound statistical measure. Here, we present the DER algorithm, available as an R package on CRAN and as an RWizard application on http://www.ipez.es/RWizard. This algorithm provides tools for differentiating assemblages on the basis of five compounds of diversity: rarity, heterogeneity, evenness, taxonomic/phylogenetic diversity and functional diversity. For all the samples, the algorithm calculates a total of 39 of the indices most often used. All indices of all samples are transformed to a scale range of between 0 and 1, and the algorithm calculates the polar coordinates of all samples with all possible combinations for all five groups of indices. Thus, for each combination, an index of rarity, heterogeneity (species richness is included in this group), evenness, taxonomic/phylogenetic diversity and functional diversity is used for each group to calculate the polar coordinates of all samples. When the polar coordinates of the samples are obtained for each combination, the convex hull and the mean Euclidean distance between samples are calculated. The algorithm selects the combination of indices with the highest value of the mean between convex hull and mean Euclidean distance between samples; priority is therefore given to maximising dispersion between the samples. The polar coordinates of the selected combination are depicted using a diagram from which it is possible to determine the differences in terms of rarity, heterogeneity, evenness, taxonomic/phylogenetic diversity and functional diversity between assemblages.},
-author = {Guisande, C{\'{a}}stor and Heine, J{\"{u}}rgen and Garc{\'{i}}a-Rosell{\'{o}}, Emilio and Gonz{\'{a}}lez-Dacosta, Jacinto and Vilas, Luis Gonz{\'{a}}lez and Perez-Schofield, Baltasar J.Garc{\'{i}}a},
-doi = {10.1016/j.ecolind.2017.05.049},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guisande et al. - 2017 - DER An algorithm for comparing species diversity between assemblages.pdf:pdf},
-issn = {1470160X},
-journal = {Ecological Indicators},
-pages = {41--46},
-title = {{DER: An algorithm for comparing species diversity between assemblages}},
-url = {http://www.sciencedirect.com/science/article/pii/S1470160X17303047},
-volume = {81},
-year = {2017}
-}
-@article{Jost2010,
-abstract = {Contrary to common belief, decomposition of diversity into independent richness and evenness components is mathematically impossible. However, richness can be decomposed into independent diversity and evenness or inequality components. The evenness or inequality component derived in this way is connected to most of the common measures of evenness and inequality in ecology and economics. This perspective justifies the derivation of measures of relative evenness, which give the amount of evenness relative to the maximum and minimum possible for a given richness. Pielou's [1] evenness measure J is shown to be such a measure.},
-author = {Jost, Lou},
-doi = {10.3390/d2020207},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2010 - The Relation between Evenness and Diversity.pdf:pdf},
-journal = {Diversity},
-number = {2},
-pages = {207--232},
-title = {{The Relation between Evenness and Diversity}},
-url = {http://www.mdpi.com/1424-2818/2/2/207},
-volume = {2},
-year = {2010}
-}
-@article{Chanthorn2017,
-abstract = {1.Seed dispersal by frugivores, particularly primates, plays an important role in structuring and maintaining tree diversity in tropical forests. However, little is known about the effect of frugivores on the diversity of saplings and large trees. 2.We used detailed census data from the fully mapped 30-ha Mo Singto forest dynamics plot in Thailand together with spatial point pattern analysis to find out if the local species richness of small (dbh {\textless}10 cm) and large (dbh ≥10 cm) trees in the neighbourhood of large trees of 52 focal species was larger or smaller than expected by an appropriate null model. 3.We then used binary data (+ or 0) on the seed dispersal network at the Mo Singto plot to test the hypothesis that the major primate frugivores, rather than other arboreal frugivores, generated patterns of locally increased species richness around their preferred diet species (i.e., accumulator effects). 4.More than half of the focal species showed accumulator effects with respect to species richness of small trees ({\textless} 10 cm in diameter), but accumulator effects with respect to large trees were weak and not consistent with those of small trees. Primate-dispersed focal species (but not hornbill- or other smaller bird-dispersed species) showed significantly larger positive effect sizes than the remaining focal species. 5.Synthesis. Our analysis suggested that primates—as major drivers of contagious seed dispersal—generate species-rich seed rain around their preferred food-tree species, which results in significantly larger local species richness of saplings. This is likely a consequence of heterospecific seed rain that reduces negative density dependence, and the presence of the accumulator pattern which persists at least until the large-size stage. Hence, extirpation of primates may result in significant changes in the diversity and spatial structure of tropical forests.},
-author = {Chanthorn, Wirong and Wiegand, Thorsten and Getzin, Stephan and Brockelman, Warren Y. and Nathalang, Anuttara},
-doi = {10.1111/1365-2745.12886},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chanthorn et al. - 2017 - Spatial patterns of local species richness reveal importance of frugivores for tropical forest diversity.pdf:pdf},
-journal = {Journal of Ecology},
-title = {{Spatial patterns of local species richness reveal importance of frugivores for tropical forest diversity}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12886},
-volume = {in press},
-year = {2017}
-}
-@article{Lurie1983,
-abstract = {In the derivation of the biomass distribution function for an ecological population critical use is made of an energetic constraint on the maximization of biomass diversity. The nature of this constraint is explored in detail using Kleiber's relation o(m) = cm 3" between animal metabolic rate o(m) and body weight m in conjunction with the Prigogine-Wiame thermodynamic paradigm for specific entropy production in biological stationary states. These two inputs fix the energetic constraint on the maximization of biomass diversity to be the constancy of the mean metabolic rate of the ecosystem. The resulting biomass distribution function is tested against observational data.},
-author = {Lurié, David and Valls, Joaquim and Wagensberg, Jorge},
-doi = {10.1016/S0092-8240(83)80032-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lurié, Valls, Wagensberg - 1983 - Thermodynamic Approach to Biomass Distribution in Ecological Systems.pdf:pdf},
-journal = {Bulletin of Mathematical Biology},
-number = {5},
-pages = {869--872},
-title = {{Thermodynamic Approach to Biomass Distribution in Ecological Systems}},
-url = {http://dx.doi.org/10.1016/S0092-8240(83)80032-9},
-volume = {45},
-year = {1983}
-}
-@phdthesis{Loubry1994,
-author = {Loubry, Denis},
-booktitle = {Biologie v{\'{e}}g{\'{e}}tale tropicale},
-publisher = {Universit{\'{e}} Paris 6},
-title = {{D{\'{e}}terminisme du comportement ph{\'{e}}nologique des arbres en for{\^{e}}t tropicale humide de Guyane fran{\c{c}}aise}},
-year = {1994}
-}
-@article{Chao2015a,
-abstract = {Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.},
-author = {Chao, Anne and Jost, Lou and Hsieh, T. C. and Ma, K. H. and Sherwin, William B. and Rollins, Lee Ann},
-doi = {10.1371/journal.pone.0125471},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2015 - Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Isla.pdf:pdf},
-journal = {PloS one},
-number = {6},
-pages = {e0125471},
-title = {{Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125471},
-volume = {10},
-year = {2015}
-}
-@article{Ayres1992,
-abstract = {River theory revisited (see Hershkowitz). Similarity of faunas on either bank increases with (a) narrowness and (b) reduction of flow rate. Similarity increases again in Amazon near mouth of river because of slow flow and islands that can be used as stepping stones for dispersal. Modern barriers may explain speciation and subspeciation. Though authors prefer a refugium-interaction-with-river explanation},
-author = {Ayres, J. M. and Clutton-Brock, T. H.},
-doi = {10.1086/285427},
-journal = {The American naturalist},
-number = {3},
-pages = {531--537},
-title = {{River Boundaries and Species Range Size in Amazonian Primates}},
-volume = {140},
-year = {1992}
-}
-@article{Karger2016,
-abstract = {Aim To provide a mechanistic and probabilistic framework for defining the species pool based on species-specific probabilities of dispersal, environmental suitability and biotic interactions within a specific temporal extent, and to show how probabilistic species pools can help disentangle the geographical structure of different community assembly processes. Innovation Probabilistic species pools provide an improved species pool definition based on probabilities in conjunction with the associated species list, which explicitly recognize the indeterminate nature of species pool membership for a given focal unit of interest and better capture real-world complexity. Probabilistic species pools provide a quantitative assessment of how dispersal, environmental or biotic factors influence estimates of species pool composition and size for a given temporal extent. Conclusions Based on one simulated and two empirical examples we demonstrate that probabilistic species pools allow us to disentangle the geographical variation in dispersal, environmental and biotic assembly processes for species assemblages in focal units. We also show that probabilistic species pools are fully compatible with traditional definitions of species pools and are applicable over a wide range of spatial and temporal extents. Additionally they are robust to missing data and provide a quantified and transparent approach to estimating the size and composition of species pools in a mechanistic way, providing a valuable tool for studies from community ecology to macroecology.},
-author = {Karger, Dirk Nikolaus and Cord, Anna F. and Kessler, Michael and Kreft, Holger and K{\"{u}}hn, Ingolf and Pompe, Sven and Sandel, Brody and {Sarmento Cabral}, Juliano and Smith, Adam B. and Svenning, Jens Christian and Tuomisto, Hanna and Weigelt, Patrick and Wesche, Karsten},
-doi = {10.1111/geb.12422},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Karger et al. - 2016 - Delineating probabilistic species pools in ecology and biogeography.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {4},
-pages = {489--501},
-title = {{Delineating probabilistic species pools in ecology and biogeography}},
-volume = {25},
-year = {2016}
-}
-@article{Kattge2011,
-abstract = {Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40{\%} of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75{\%} of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.},
-author = {Kattge, J. and D{\'{i}}az, Sandra and Lavorel, Sandra and Prentice, I. C. and Leadley, P. and B{\"{o}}nisch, G. and Garnier, Eric and Westoby, Mark and Reich, Peter B. and Wright, Ian J. and Cornelissen, Johannes H. C. and Violle, Cyrille and Harrison, Susan P. and {Van Bodegom}, P. M. and Reichstein, M. and Enquist, Brian J. and Soudzilovskaia, N. A. and Ackerly, David D. and Anand, Madhur and Atkin, O. K. and Bahn, M. and Baker, Timothy R. and Baldocchi, D. and Bekker, R. and Blanco, Carolina C. and Blonder, Benjamin and Bond, W. J. and Bradstock, R. and Bunker, D. E. and Casanoves, Fernando and Cavender-Bares, Jeannine and Chambers, Jeffrey Q. and Chapin, F. Stuart III and Chave, J{\'{e}}r{\^{o}}me and Coomes, David Anthony and Cornwell, William K. and Craine, J. M. and Dobrin, B. H. and Duarte, L. and Durka, W. and Elser, J. and Esser, G. and Estiarte, M. and Fagan, W. F. and Fang, J. and Fern{\'{i}}ndez-M{\'{e}}ndez, F. and Fidelis, A. and Finegan, B. and Flores, Olivier and Ford, H. and Frank, D. and Freschet, G. T. and Fyllas, N. M. and Gallagher, R. V. and Green, W. A. and Gutierrez, A. G. and Hickler, T. and Higgins, S. I. and Hodgson, J. G. and Jalili, A. and Jansen, S. and Joly, C. A. and Kerkhoff, A. J. and Kirkup, D. and Kitajima, K. and Kleyer, M. and Klotz, S. and Knops, J. M. H. and Kramer, K. and K{\"{u}}hn, I. and Kurokawa, H. and Laughlin, D. and Lee, T. D. and Leishman, M. and Lens, F. and Lenz, T. and Lewis, Simon L. and Lloyd, J. and Llusi{\`{a}}, J. and Louault, F. and Ma, S. and Mahecha, M. D. and Manning, Peter and Massad, T. and Medlyn, B. E. and Messier, Julie and Moles, Angela T. and M{\"{u}}ller, Sandra C. and Nadrowski, K. and Naeem, Shahid and Niinemets, {\"{U}}lo and N{\"{o}}llert, S. and N{\"{u}}ske, A. and Ogaya, R. and Oleksyn, J. and Onipchenko, V. G. and Onoda, Y. and Ordo{\~{n}}ez, J. and Overbeck, G. and Ozinga, W. A. and Pati{\~{n}}o, Sandra and Paula, S. and Pausas, J. G. and Pe{\~{n}}uelas, J. and Phillips, Oliver L. and Pillar, V. and Poorter, Hendrik and Poorter, Lourens and Poschlod, P. and Prinzing, A. and Proulx, R. and Rammig, A. and Reinsch, S. and Reu, B. and Sack, L. and Salgado-Negret, B. and Sardans, J. and Shiodera, S. and Shipley, Bill and Siefert, A. and Sosinski, E. and Soussana, Jean-Fran{\c{c}}ois and Swaine, E. and Swenson, Nathan G. and Thompson, Ken and Thornton, P. and Waldram, M. and Weiher, E. and White, Mark and White, S. and Wright, S. Joseph and Yguel, B. and Zaehle, S. and Zanne, Amy E. and Wirth, Christian},
-doi = {10.1111/j.1365-2486.2011.02451.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kattge et al. - 2011 - TRY – a global database of plant traits.pdf:pdf},
-journal = {Global Change Biology},
-number = {9},
-pages = {2905--2935},
-title = {{TRY – a global database of plant traits}},
-url = {http://dx.doi.org/10.1111/j.1365-2486.2011.02451.x},
-volume = {17},
-year = {2011}
-}
-@article{Forget1994,
-abstract = {The recruitment pattern of Vouacapoua americana and the relationship between growth and survival of recruits were analysed during 1984-91 on two 2500 m2 plots, one with and one without free soil drainage, at Ecerex Research Field Station, French Guiana. Most seeds and seedlings below two adult trees in the plots died within 6-8 months of establishment. Virtually all seedlings still alive several months after fruiting arose from seeds that were buried by scatterhoarding rodents. Because rodents do not disperse seeds a great distance and V. americana seedlings survive well in the shaded understorey, offspring recruitment was more dense near the adults than further away. A significantly lower proportion of newly established seedlings died on freely drained soil than where drainage was blocked; mortality was caused by damping-off fungi. First-year survival of seedlings from scatterhoarded seeds and growth rates for understorey seedlings from 1984 to 1986 were higher on freely drained soil than on blocked soil. Long-term offspring survival was similar on both plots, while height increment was significantly greater on the freely drained plots than on the poorly drained soil. There was a significant negative relationship between the initial seedling density and proportion of survival on both plots within 6-8 months of establishment. However, there was no evidence of long-term compensatory mortality; the greater the initial density, the greater the final density of recruits surviving through years. The V. americana recruitment pattern appears typical of a partially repelled syndrome with recruits growing both near adults and further away. High V. americana tree density on soil with good drainage, as reported in the literature, is likely to result from better environmental conditions for early seedling survival and long-term growth of recruits.},
-author = {Forget, Pierre-Michel},
-doi = {10.2307/2389235},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Forget - 1994 - Recruitment pattern of Vouacapoua americana (Caesalpiniaceae), a rodent-dispersed tree species in French Guiana.pdf:pdf},
-journal = {Biotropica},
-number = {4},
-pages = {408--419},
-title = {{Recruitment pattern of Vouacapoua americana (Caesalpiniaceae), a rodent-dispersed tree species in French Guiana}},
-url = {https://www.jstor.org/stable/2389235},
-volume = {26},
-year = {1994}
-}
-@book{Magurran1988,
-address = {Princeton, NJ},
-author = {Magurran, Anne E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Magurran - 1988 - Ecological diversity and its measurement.pdf:pdf},
-publisher = {Princeton University Press},
-title = {{Ecological diversity and its measurement}},
-year = {1988}
-}
-@article{Sveikauskas1975,
-abstract = {I. The increase in productivity with city size, 393. — II. The labor productivity of cities, 396. — III. The contributions of Hicks-neutral productivity and capital intensity, 401. — IV. The direction of causality, 406. — V. Conclusions, 410. — Appendix A: choice of the industries included in this study, 411. — Appendix B: evidence relating to the capital-labor ratio in cities of different size, 412.},
-author = {Sveikauskas, Leo},
-doi = {10.2307/1885259},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sveikauskas - 1975 - The productivity of cities.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {3},
-pages = {393--413},
-title = {{The productivity of cities}},
-url = {https://doi.org/10.2307/1885259},
-volume = {89},
-year = {1975}
-}
-@article{Morphet1997,
-abstract = {A method is presented for the identification and location of clusters in data reported in small areal units. The areal units are aggregated into zones which are not prespecified at the outset and which may be of any shape or size. A statistical distribution is described against which any apparent clusters in the zones can be assessed for statistical significance. Monte Carlo methods are used to derive the distribution, and it is argued that complex null hypotheses can be represented in this way. In this approach the critical distinction between prespecified and constructed areas or zones of interest is recognised, and is shown to circumvent some of the difficulties usually associated with modifiable areal units.},
-author = {Morphet, C. S.},
-doi = {10.1068/a291039},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Morphet - 1997 - A statistical method for the identification of spatial clusters.pdf:pdf},
-journal = {Environment and Planning A},
-number = {6},
-pages = {1039--1055},
-title = {{A statistical method for the identification of spatial clusters}},
-url = {http://epn.sagepub.com/content/29/6/1039.short},
-volume = {29},
-year = {1997}
-}
-@article{Iknayan2014,
-abstract = {Estimates of species richness and diversity are central to community and macroecology and are frequently used in conservation planning. Commonly used diversity metrics account for undetected species primarily by controlling for sampling effort. Yet the probability of detecting an individual can vary among species, observers, survey methods, and sites. We review emerging methods to estimate alpha, beta, gamma, and metacommunity diversity through hierarchical multispecies occupancy models (MSOMs) and multispecies abundance models (MSAMs) that explicitly incorporate observation error in the detection process for species or individuals. We examine advantages, limitations, and assumptions of these detection-based hierarchical models for estimating species diversity. Accounting for imperfect detection using these approaches has influenced conclusions of comparative community studies and creates new opportunities for testing theory.},
-author = {Iknayan, Kelly J. and Tingley, Morgan W. and Furnas, Brett J. and Beissinger, Steven R.},
-doi = {10.1016/j.tree.2013.10.012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Iknayan et al. - 2014 - Detecting diversity emerging methods to estimate species diversity.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {2},
-pages = {97--106},
-title = {{Detecting diversity: emerging methods to estimate species diversity}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534713002619},
-volume = {29},
-year = {2014}
-}
-@article{Lamb2015,
-abstract = {The flaws of using traditional planar point-pattern analysis techniques with network constrained points have been thoroughly explored in the literature. Because of this, new network-based measures have been introduced for their planar analogues, including the network based K-function. These new measures involve the calculation of network distances between point events rather than traditional Euclidean distances. Some have suggested that the underlying structure of a network, such as whether it includes directional constraints or speed limits, may be considered when applying these methods. How different network structures might affect the results of the network spatial statistics is not well understood. This article examines the results of network K-functions when taking into consideration network distances for three different types of networks: the original road network, topologically correct networks, and directionally constrained networks. For this aim, four scenarios using road networks from Tampa, Florida and New York City, New York were used to test how network constraints affected the network K-function. Depending on which network is under consideration, the underlying network structure could impact the interpretation. In particular, directional constraints showed reduced clustering across the different scenarios. Caution should be used when selecting the road network, and constraints, for a network K-function analysis.},
-author = {Lamb, David S and Downs, Joni A. and Lee, Chanyoung},
-doi = {10.1111/tgis.12157},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lamb, Downs, Lee - 2015 - The network K-function in context examining the effects of network structure on the network K-function.pdf:pdf},
-journal = {Transactions in GIS},
-number = {3},
-pages = {448--460},
-title = {{The network K-function in context : examining the effects of network structure on the network K-function}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/tgis.12157/full},
-volume = {20},
-year = {2016}
-}
-@article{Fratesi2008,
-abstract = {The degree of localization of manufacturing, defined as the excess geographic concentration remaining after correcting for both sectoral concentration and the agglomeration of overall economic activity, has recently gained new techniques of measurement in the form of indexes and numerical methods. These techniques are illustrated, compared, and theoretically discussed to show that they are consistent advancements, but none is yet able to satisfy all desirable properties. The measurement of localization would be more interesting if it could be related to economic processes and not limited to simple observational aspects. In achieving this, there are a number of complications, which are reviewed in the paper. Among these, the choice of the right sectoral scale at which these measures have to be applied is normally given too little importance. The second part of this paper advocates that this is a complex issue, since no digit level is appropriate for all industries. Moreover, different aggregations of narrowly defined subsectors may be more suitable than the standard industrial classifications. This is supported by an exploratory analysis, in two British sectors, based on the investigation of possible localization reasons identified in recent taxonomies. As the many localization measurement techniques have become available, it is recommended that they be applied to sector studies, and not confined to countrywide extensive explorations of all sectors.},
-author = {Fratesi, Ugo},
-doi = {10.1068/a39223},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fratesi - 2008 - Issues in the measurement of localization.pdf:pdf},
-journal = {Environment and Planning A},
-number = {3},
-pages = {733--758},
-title = {{Issues in the measurement of localization}},
-url = {http://www.envplan.com/abstract.cgi?id=a39223},
-volume = {40},
-year = {2008}
-}
-@article{Krishnamani2004,
-abstract = {Estimating species richness in large biomes is a central challenge in ecology and conservation biology. However, accurate census data is often available only from small discrete plots distributed within the biome. Using tree species richness data collected from 48 plots (0.25 ha each) widely distributed through 60 000 km(2) in the rainforests of the Western Ghats of southern India, we test the application of a proposed method for estimating species richness at large scales from measured species commonalities between pairs of censused plots. We show that the method allows extrapolation of species richness from a scale of 0.25 ha plots to that of the entire biome, or 10(5) km(2).},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Krishnamani, R. and Kumar, A. and Harte, John},
-doi = {10.1111/j.0906-7590.2004.03790.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Krishnamani, Kumar, Harte - 2004 - Estimating species richness at large spatial scales using data from small discrete plots.pdf:pdf},
-journal = {Ecography},
-number = {5},
-pages = {637--642},
-title = {{Estimating species richness at large spatial scales using data from small discrete plots}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2004.03790.x/full},
-volume = {27},
-year = {2004}
-}
-@article{MacArthur1955,
-author = {MacArthur, Robert H.},
-doi = {doi:10.2307/1929601},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacArthur - 1955 - Fluctuations of Animal Populations and a Measure of Community Stability.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {533--536},
-title = {{Fluctuations of Animal Populations and a Measure of Community Stability}},
-url = {http://www.esajournals.org/doi/abs/10.2307/1929601},
-volume = {36},
-year = {1955}
-}
-@article{Pausas2003,
-abstract = {In the framework of land use changes in the Mediterranean area, I asked to what extent different landscape structures might determine long-term dynamics in Mediterranean ecosystems. To answer this question, a spatially explicit model was developed (the MELCA model), incorporating two functional types of woody species dominant in Mediterranean ecosystems: a resprouter (R) and a non-resprouter fire-recruiter (seeders, S). The model was used as a tool for generating hypotheses on the possible consequences of different landscape scenarios. Thus, five different hierarchically structured random landscapes were generated, all having the same cover for the two functional types but different landscape structure (ranging from highly heterogeneous to homogeneous landscapes). After a 100-yr simulation, plant cover and spatial pattern had changed and the changes were different for the different initial spatial configurations, suggesting that long-term vegetation dynamics is spatially dependent (the resultant dynamics are sensitive to the initial spatial structure). In the landscapes where R-type species had a low number of large patches and S-species had a large number of small patches, the number of R-patches increased and their size decreased, while the number of S-patches decreased. In these cases, the final cover of the two types changed little from the initial cover. Landscapes with a large number of small R-patches interspersed with S-patches had a decrease in the number of R-patches, an increase in the number of S-patches and a decrease in the size of S-patches. In these landscapes, final cover was significantly changed, increasing in R-type and decreasing in S-type species. These results suggest that low spatial autocorrelation (low aggregation) favours R-type species. Implications for land management are also discussed.},
-author = {Pausas, J. G.},
-doi = {10.1111/j.1654-1103.2003.tb02162.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pausas - 2003 - The effect of landscape pattern on Mediterranean vegetation dynamics A modelling approach using functional types(2).pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {365--374},
-title = {{The effect of landscape pattern on Mediterranean vegetation dynamics: A modelling approach using functional types}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2003.tb02162.x/abstract},
-volume = {14},
-year = {2003}
-}
-@article{Takacs1986,
-abstract = {A point configuration is supposed to be from a homogeneous Gibbsian point process with a pair–potential with finite range. The pair–potential is of the form of a step–function. An estimator for this pair–potential is derived.},
-author = {Takacs, R.},
-doi = {10.1080/02331888608801956},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Takacs - 1986 - Estimator for the pair-potential of a gibbsian point process.pdf:pdf},
-journal = {Statistics},
-number = {3},
-pages = {429--433},
-title = {{Estimator for the pair-potential of a gibbsian point process}},
-url = {http://dx.doi.org/10.1080/02331888608801956},
-volume = {17},
-year = {1986}
-}
-@article{Wang2011,
-abstract = {We introduce an R package SPECIES for species richness or diversity estimation. This package provides simple R functions to compute point and condfience interval estimates of species number from a few nonparametric and semi-parametric methods. For the methods based on nonparametric maximum likelihood estimation, the R functions are wrappers for Fortran codes for better efficiency. All functions in this package are illustrated using real data sets.},
-author = {Wang, Ji-Ping},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wang - 2011 - SPECIES An R Package for Species Richness Estimation.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {9},
-pages = {1--15},
-title = {{SPECIES: An R Package for Species Richness Estimation}},
-url = {http://www.jstatsoft.org/v40/i09},
-volume = {40},
-year = {2011}
-}
-@inproceedings{Guyon1999,
-address = {M{\'{e}}rida, Venezuela},
-author = {Guyon, Xavier},
-booktitle = {Ecole d'{\'{e}}t{\'{e}} de Math{\'{e}}matiques},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guyon - 1999 - M{\'{e}}thodes num{\'{e}}riques par cha{\^{i}}nes de Markov.pdf:pdf},
-keywords = {Guyon (1999).pdf},
-mendeley-tags = {Guyon (1999).pdf},
-pages = {97},
-publisher = {Universit{\'{e}} Paris I et Universidad de Los Andes},
-title = {{M{\'{e}}thodes num{\'{e}}riques par cha{\^{i}}nes de Markov}},
-url = {ftp://ftp.univ-paris1.fr/pub/SAMOS/cours/ecoleete.pdf},
-year = {1999}
-}
-@article{Harkness1983,
-abstract = {The nesting behaviour of two species of ant (Cataglyphis bicolor and Messor wasmanni) is investigated by regarding their nests as a bivariate spatial point pattern. When the nests of each species are considered separately, those of the Messors are found to be more regularly spaced than would be the case if they were located at random. There is no strong evidence of such inhibition between the Cataglyphis nests. The possibility that the positions of the nests of Cataglyphis ants are dependent upon those of the Messors is suggested on biological grounds, and is investigated by various methods. No clear evidence for such an association is established.},
-author = {Harkness, R. D. and Isham, Valerie},
-doi = {10.2307/2347952},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harkness, Isham - 1983 - A Bivariate Spatial Point Pattern of Ants' Nests.pdf:pdf},
-journal = {Journal of the Royal Statistical Society. Series C (Applied Statistics)},
-number = {3},
-pages = {293--303},
-title = {{A Bivariate Spatial Point Pattern of Ants' Nests}},
-url = {http://www.jstor.org/stable/2347952},
-volume = {32},
-year = {1983}
-}
-@article{Osazuwa-Peters2015,
-abstract = {Selective logging of tropical forests is increasing in extent and intensity. The duration over which impacts of selective log- ging persist, however, remains an unresolved question, particularly for African forests. Here, we investigate the extent to which a past selective logging event continues to leave its imprint on different components of an East African forest 45 years later. We inventoried 2358 stems ≥10 cm in diameter in 26 plots (200 m × 10 m) within a 5.2 ha area in Kibale National Park, Uganda, in logged and unlogged forest. In these surveys, we characterized the forest light environment, taxonomic composition, functional trait composition using three traits (wood density, maximum height and maximum diameter) and forest structure based on three measures (stem density, total basal area and total above-ground biomass). In comparison to unlogged forests, selectively logged forest plots in Kibale National Park on average had higher light lev- els, different structure characterized by lower stem density, lower total basal area and lower above-ground biomass, and a distinct taxonomic composition driven primarily by changes in the relative abundance of species. Conversely, selectively logged forest plots were like unlogged plots in functional composition, having similar community-weighted mean values for wood density, maximum height and maximum diameter. This similarity in functional composition irrespective of log- ging history may be due to functional recovery of logged forest or background changes in functional attributes of unlogged forest. Despite the passage of 45 years, the legacy of selective logging on the tree community in Kibale National Park is still evident, as indicated by distinct taxonomic and structural composition and reduced carbon storage in logged forest com- pared with unlogged forest. The effects of selective logging are exerted via influences on tree demography rather than functional trait composition},
-author = {Osazuwa-Peters, Oyomoare L. and Chapman, Colin A. and Zanne, Amy E.},
-doi = {10.1093/conphys/cov012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Osazuwa-Peters, Chapman, Zanne - 2015 - Selective logging does the imprint remain on tree structure and composition after 45 years(2).pdf:pdf},
-journal = {Conservation Physiology},
-number = {1},
-pages = {cov012},
-title = {{Selective logging: does the imprint remain on tree structure and composition after 45 years?}},
-volume = {3},
-year = {2015}
-}
-@article{Sui2002,
-abstract = {This paper examines individual voter turn-out and its putative relationship with voting outcomes at the voting precinct level. Via a GIS-based address matching procedure, we were able to georeference individual voters (registered voters who casted their votes) and non-voters (those registered voters who did not cast their votes) for three recent local referenda in College Station, Texas. We then conducted a scale-sensitive, second-order spatial analysis for the spatial distribution of voter turn-outs, followed by a spatial clustering analysis of the voting results using Getis–Ord's Gi statistic. We found that the extent of neighborhood effects in local elections is heavily influenced by the voter turn-out. If voter turn-out is clustered at intermediate and large scale, voting results tend to be clustered and also exhibit a sharp polarization between high and low values. If voter turn-out tends to be uniform/regular at intermediate scales but randomly distributed at both small and large scales, there appears to be less clustering in the voting results and thus lack of the neighborhood effect. If the voter turn-out pattern is mixeduniform/ regular at the small scale, random at the intermediate scale, but clustered at the large scale, the voting results show a stronger neighborhood effect.},
-author = {Sui, Danile Z. and Hugill, Peter J.},
-doi = {10.1016/S0962-6298(01)00054-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sui, Hugill - 2002 - A GIS-based spatial analysis on neighborhood effects and voter turn-out - a case study in College Station, Texas.pdf:pdf},
-journal = {Political Geography},
-number = {2},
-pages = {159--173},
-title = {{A GIS-based spatial analysis on neighborhood effects and voter turn-out: a case study in College Station, Texas}},
-url = {http://www.sciencedirect.com/science/article/pii/S0962629801000543},
-volume = {21},
-year = {2002}
-}
-@article{Alonso2004,
-abstract = {In the context of neutral theories of community ecology, a novel genealogy-based framework has recently furnished an analytic extension of Ewens' sampling multivariate abundance distribution, which also applies to a random sample from a local community. Here, instead of taking a multivariate approach, we further develop the sampling theory of Hubbell's neutral spatially implicit theory and derive simple abundance distributions for a random sample both from a local community and a metacommunity. Our result is given in terms of the average number of species with a given abundance in any randomly extracted sample. Contrary to what has been widely assumed, a random sample from a metacommunity is not fully described by the Fisher log-series, but by a new distribution. This new sample distribution matches the log-series expectation at high biodiversity values ($\theta$ {\textgreater} 1) but clearly departs from it for species-poor metacommunities ($\theta$ {\textless} 1). Our theoretical framework should be helpful in the better assessment of diversity and testing of the neutral theory by using abundance data.},
-author = {Alonso, David and McKane, Alan J.},
-doi = {10.1111/j.1461-0248.2004.00640.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alonso, McKane - 2004 - Sampling Hubbell's neutral theory of biodiversity.pdf:pdf},
-journal = {Ecology Letters},
-number = {10},
-pages = {901--910},
-title = {{Sampling Hubbell's neutral theory of biodiversity}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2004.00640.x},
-volume = {7},
-year = {2004}
-}
-@article{Zinger2014,
-abstract = {The taxa-area relationship (TAR) and the distance-decay relationship (DDR) both describe spatial turnover of taxa and are central patterns of biodiversity. Here, we compared TAR and DDR of bacterial communities across different marine realms and ecosystems at the global scale. To obtain reliable global estimates for both relationships, we quantified the poorly assessed effects of sequencing depth, rare taxa removal and number of sampling sites. Slope coefficients of bacterial TARs were within the range of those of plants and animals, whereas slope coefficients of bacterial DDR were much lower. Slope coefficients were mostly affected by removing rare taxa and by the number of sampling sites considered in the calculations. TAR and DDR slope coefficients were overestimated at sequencing depth {\textless}4000 sequences per sample. Noticeably, bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors. Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared with pelagic ecosystems. Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights, at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.},
-author = {Zinger, Lucie and Boetius, A. and Ramette, A.},
-doi = {10.1111/mec.12640},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zinger, Boetius, Ramette - 2014 - Bacterial taxa-area and distance-decay relationships in marine environments.pdf:pdf},
-journal = {Molecular Ecology},
-number = {4},
-pages = {954--964},
-title = {{Bacterial taxa-area and distance-decay relationships in marine environments}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/mec.12640/abstract;jsessionid=C0B6B2D024427932BD267B0C16E07061.f02t04},
-volume = {23},
-year = {2014}
-}
-@article{Purvis2000,
-abstract = {The term 'biodiversity' is a simple contraction of 'biological diversity', and at first sight the concept is simple too: biodiversity is the sum total of all biotic variation from the level of genes to ecosystems. The challenge comes in measuring such a broad concept in ways that are useful. We show that, although biodiversity can never be fully captured by a single number, study of particular facets has led to rapid, exciting and sometimes alarming discoveries. Phylogenetic and temporal analyses are shedding light on the ecological and evolutionary processes that have shaped current biodiversity. There is no doubt that humans are now destroying this diversity at an alarming rate. A vital question now being tackled is how badly this loss affects ecosystem functioning. Although current research efforts are impressive, they are tiny in comparison to the amount of unknown diversity and the urgency and importance of the task.},
-author = {Purvis, Andy and Hector, Andy},
-doi = {10.1038/35012221},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Purvis, Hector - 2000 - Getting the measure of biodiversity.pdf:pdf},
-journal = {Nature},
-number = {6783},
-pages = {212--9},
-title = {{Getting the measure of biodiversity.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/10821281},
-volume = {405},
-year = {2000}
-}
-@article{Ozinga2005,
-abstract = {Despite recent modelling approaches integrating the effects of niche-based processes and dispersal-based processes on local plant species composition, their relative importance is still not clear. We test whether the predictability of local species composition from environmental conditions is influenced by dispersal traits. We analyzed a large database with co-occurrence data, using ordination techniques (DCA and CCA) to identify the major environmental determinants of species composition. The percentage of explained variance in occurrence was quantified for individual species with CCA. Effects of life-history traits on the predictability of occurrence patterns were tested by means of regression analysis, using a generalized linear models approach. The results reveal close correlations between species composition and environmental conditions, implying that the predictability of the set of species that might occur in a given environmental setting ("habitat species pool") is high. The habitat species pool, however, reflects the potential species composition, and not the actual local situation. At the level of individual species, a large proportion ({\textgreater}90{\%}) of the variation in occurrence remained unexplained. Predictability of species occurrence patterns was increased by a greater capacity for long-distance dispersal, greater adult longevity and the capacity to build a persistent seed bank. The results indicate that the predictability of species composition from environmental conditions is reduced by a few orders of magnitude by dispersal limitation and that poor dispersers are underrepresented.},
-author = {Ozinga, Wim A. and Schamin{\'{e}}e, Joop H.J. and Bekker, Ren{\'{e}}e M. and Bonn, Susanne and Poschlod, Peter and Tackenberg, Oliver and Bakker, Jan and {Van Groenendael}, Jan M.},
-doi = {10.1111/j.0030-1299.2005.13632.x},
-isbn = {0030-1299},
-issn = {00301299},
-journal = {Oikos},
-number = {3},
-pages = {555--561},
-pmid = {3244},
-title = {{Predictability of plant species composition from environmental conditions is constrained by dispersal limitation}},
-volume = {108},
-year = {2005}
-}
-@article{Daroczy1970,
-abstract = {The concept of information functions of type $\beta$ ($\beta$ {\textgreater} 0) is introduced and discussed. By means of these information functions the entropies of type $\beta$ are defined. These entropies have a number of interesting algebraic and analytic properties similar to Shannon's entropy. The capacity of type $\beta$ ($\beta$ {\textgreater} 1) of a discrete constant channel is defined by means of the entropy of type $\beta$. Examples are given for the computation of the capacity of type $\beta$, from which the Shannon's capacity can be derived as the limiting case $\beta$ = 1.},
-author = {Dar{\'{o}}czy, Zolt{\'{a}}n},
-doi = {10.1016/s0019-9958(70)80040-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dar{\'{o}}czy - 1970 - Generalized information functions.pdf:pdf},
-journal = {Information and Control},
-number = {1},
-pages = {36--51},
-title = {{Generalized information functions}},
-url = {http://www.sciencedirect.com/science/article/pii/S0019995870800407},
-volume = {16},
-year = {1970}
-}
-@article{Hutchinson1959,
-abstract = {This database allows users to search the complete printed text of Acta Sanctorum, from the edition published in sixty-eight volumes by the Soci�t� des Bollandistes in Antwerp and Brussels. It contains the entire Acta Sanctorum, including all prefatory material, original texts, critical apparatus and indices; Bibliotheca Hagiographica Latina reference numbers and references for scholars are also included.},
-author = {Hutchinson},
-journal = {the american naturalist},
-number = {870},
-pages = {145--159},
-title = {{Homage to Santa Rosalia, or why are there so many different kinds of animals?}},
-volume = {93},
-year = {1959}
-}
-@article{Axtell2001,
-abstract = {Analyses of firm sizes have historically used data that included limited samples of small firms, data typically described by lognormal distributions. Using data on the entire population of tax-paying firms in the United States, I show here that the Zipf distribution characterizes firm sizes: the probability a firm is larger than size s is inversely proportional to s. These results hold for data from multiple years and for various definitions of firm size.},
-archivePrefix = {arXiv},
-arxivId = {-},
-author = {Axtell, Robert L.},
-doi = {10.1126/science.1062081},
-eprint = {-},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Axtell - 2001 - Zipf distribution of U.S. firm sizes.pdf:pdf},
-journal = {Science},
-number = {5536},
-pages = {1818--1820},
-title = {{Zipf distribution of U.S. firm sizes}},
-url = {http://science.sciencemag.org/content/293/5536/1818},
-volume = {293},
-year = {2001}
-}
-@article{Legendre2013,
-abstract = {Beta diversity can be measured in different ways. Among these, the total variance of the community data table Y can be used as an estimate of beta diversity. We show how the total variance of Y can be calculated either directly or through a dissimilarity matrix obtained using any dissimilarity index deemed appropriate for pairwise comparisons of community composition data. We addressed the question of which index to use by coding 16 indices using 14 properties that are necessary for beta assessment, comparability among data sets, sampling issues and ordination. Our comparison analysis classified the coefficients under study into five types, three of which are appropriate for beta diversity assessment. Our approach links the concept of beta diversity with the analysis of community data by commonly used methods like ordination and anova. Total beta can be partitioned into Species Contributions (SCBD: degree of variation of individual species across the study area) and Local Contributions (LCBD: comparative indicators of the ecological uniqueness of the sites) to Beta Diversity. Moreover, total beta can be broken up into within- and among-group components by manova, into orthogonal axes by ordination, into spatial scales by eigenfunction analysis or among explanatory data sets by variation partitioning.},
-author = {Legendre, Pierre and {De C{\'{a}}ceres}, Miquel},
-doi = {10.1111/ele.12141},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, De C{\'{a}}ceres - 2013 - Beta diversity as the variance of community data Dissimilarity coefficients and partitioning.pdf:pdf},
-journal = {Ecology Letters},
-number = {8},
-pages = {951--963},
-title = {{Beta diversity as the variance of community data: Dissimilarity coefficients and partitioning}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12141/abstract},
-volume = {16},
-year = {2013}
-}
-@incollection{Combes2015,
-address = {Amsterdam},
-author = {Combes, Pierre-Philippe and Gobillon, L.},
-booktitle = {Handbook of Urban and Regional Economics},
-chapter = {5},
-editor = {Duranton, Gilles and Henderson, J. Vernon and Strange, William C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Combes, Gobillon - 2015 - The empirics of agglomeration economies.pdf:pdf},
-pages = {247--348},
-publisher = {Elsevier},
-title = {{The empirics of agglomeration economies}},
-volume = {5},
-year = {2015}
-}
-@article{Dewar2008,
-abstract = {Recently there has been growing interest in the use of maximum relative entropy (MaxREnt) as a tool for statistical inference in ecology. In contrast, here we propose MaxREnt as a tool for applying statistical mechanics to ecology. We use MaxREnt to explain and predict species abundance patterns in ecological communities in terms of the most probable behaviour under given environmental constraints, in the same way that statistical mechanics explains and predicts the behaviour of thermodynamic systems. We show that MaxREnt unifies a number of different ecological patterns: (i) at relatively local scales a unimodal biodiversity-productivity relationship is predicted in good agreement with published data on grassland communities, (ii) the predicted relative frequency of rare vs. abundant species is very similar to the empirical lognormal distribution, (iii) both neutral and non-neutral species abundance patterns are explained, (iv) on larger scales a monotonic biodiversity-productivity relationship is predicted in agreement with the species-energy law, (v) energetic equivalence and power law self-thinning behaviour are predicted in resource-rich communities. We identify mathematical similarities between these ecological patterns and the behaviour of thermodynamic systems, and conclude that the explanation of ecological patterns is not unique to ecology but rather reflects the generic statistical behaviour of complex systems with many degrees of freedom under very general types of environmental constraints.},
-author = {Dewar, Roderick C. and Port{\'{e}}, Annabel},
-doi = {10.1016/j.jtbi.2007.12.007},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dewar, Port{\'{e}} - 2008 - Statistical mechanics unifies different ecological patterns.pdf:pdf},
-journal = {Journal of theoretical biology},
-number = {3},
-pages = {389--403},
-title = {{Statistical mechanics unifies different ecological patterns}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/18237750},
-volume = {251},
-year = {2008}
-}
-@article{Kempton1978,
-abstract = {Two popular diversity indices, Simpson's index Y and the Information index H, are compared with a new measure Q based on the inter-quartile slope of the cumulative species abundance curve. It is assumed that interest extends to characterizing the site environment; the population present at the instant of sampling is considered to be only one of a range of possible populations which the site could support. Expressions are derived for the expectations and variances of the three sample statistics a{\$}{\_}Y{\$}, a{\$}{\_}H{\$}, and a{\$}{\_}Q{\$} when the species abundances are gamma variates. Q is a more informative measure than H or Y. Both H and Y depend greatly on the abundances of the commonest species, which may fluctuate widely from year to year. Q depends on the more stable species with median abundance and discriminates better between sites than H or Y; it can be recommended when sites are to be compared. The expected value of Q is expressed in terms of the parameters of the gamma, lognormal and log-series models and is shown to be much more robust than H or Y to the particular choice of model. For the log-series model, E(Q) is represented by the parameter {\$}\backslashalpha{\$}, while for the lognormal E(Q) = 0.371 T/{\$}\backslashsigma{\$}, where T is the number of species in the population and {\$}\backslashsigma{\$} is the standard deviation of logged abundances. a{\$}{\_}Q{\$} may be biased in small samples, though the bias should be fairly small when more than 50{\%} of a species are present in the sample. Absence of small sample bias should not be an overriding criterion in selecting a diversity index since small samples will at best only allow the crudest comparisons between communities.},
-author = {Kempton, R. A. and Wedderburn, R. W. M.},
-doi = {10.2307/2529585},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kempton, Wedderburn - 1978 - A comparison of three measures of species diversity.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {25--37},
-title = {{A comparison of three measures of species diversity}},
-url = {https://www.jstor.org/stable/2529585},
-volume = {34},
-year = {1978}
-}
-@article{Lin1991,
-abstract = {A novel class of information-theoretic divergence measures based on the Shannon entropy is introduced. Unlike the well-known Kullback divergences, the new measures do not require the condition of absolute continuity to be satisfied by the probability distributions involved. More importantly, their close relationship with the variational distance and the probability of misclassification error are established in terms of bounds. These bounds are crucial in many applications of divergence measures. The measures are also well characterized by the properties of nonnegativity, finiteness, semiboundedness, and boundedness},
-author = {Lin, Jianhua},
-doi = {10.1109/18.61115},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lin - 1991 - Divergence Measures Based on the Shannon Entropy.pdf:pdf},
-journal = {IEEE Transactions on Information Theory},
-number = {1},
-pages = {145--151},
-title = {{Divergence Measures Based on the Shannon Entropy}},
-url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=61115},
-volume = {37},
-year = {1991}
-}
-@article{Magurran2016,
-author = {Magurran, Anne E.},
-doi = {10.1126/science.aad6758},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Magurran - 2016 - How ecosystems change.pdf:pdf},
-issn = {0036-8075},
-journal = {Science},
-number = {6272},
-pages = {448--449},
-title = {{How ecosystems change}},
-url = {http://science.sciencemag.org/content/351/6272/448.full},
-volume = {351},
-year = {2016}
-}
-@incollection{Dixon2002,
-abstract = {Ripley's K function summarizes spatial point process data. It can be used to describe a set of locations, test hypotheses about patterns, and estimate parameters in a spatial point process model. For a stationary point process, K(t) is the expected number of additional points within distance t of a focal point divided by the intensity of the process. A univariate version is used for one set of locations and a multivariate version is used when points can be labeled by a small number of groups. This article reviews the properties of Ripley's K function and two related functions, then illustrates the computation and interpretation using data on the locations of trees in a swamp hardwood forest.},
-address = {New York},
-author = {Dixon, Philip M.},
-booktitle = {The encyclopaedia of environmetrics},
-doi = {10.1002/9780470057339.var046.pub2},
-editor = {{El Shaarawi}, A H and Piergorsch, W W},
-pages = {1803--1976},
-publisher = {John Wiley {\&} Sons},
-title = {{Ripley's K function}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470057339.var046.pub2/full},
-year = {2002}
-}
-@article{Baraloto2010,
-abstract = {1. Despite considerable interest in the application of plant functional traits to questions of community assembly and ecosystem structure and function, there is no consensus on the appropriateness of sampling designs to obtain plot-level estimates in diverse plant communities. 2. We measured 10 plant functional traits describing leaf and stem morphology and ecophysiology for all trees in nine 1-ha plots in terra firme lowland tropical rain forests of French Guiana (N = 4709). 3.We calculated, by simulation, the mean and variance in trait values for each plot and each trait expected under seven sampling methods and a range of sampling intensities. Simulated sampling methods included a variety of spatial designs, as well as the application of existing data base values to all individuals of a given species. 4. For each trait in each plot, we defined a performance index for each sampling design as the proportion of resampling events that resulted in observed means within 5{\%} of the true plot mean, and observed variance within 20{\%}of the true plot variance. 5. The relative performance of sampling designs was consistent for estimations of means and variances. Data base use had consistently poor performance for most traits across all plots, whereas sampling one individual per species per plot resulted in relatively high performance. We found few differences among different spatial sampling strategies; however, for a given strategy, increased intensity of sampling resulted in markedly improved accuracy in estimates of trait mean and variance. 6. We also calculated the financial cost of each sampling design based on data from our ‘every individual per plot' strategy and estimated the sampling and botanical effort required. The relative performance of designs was strongly positively correlated with relative financial cost, suggesting that sampling investment returns are relatively constant. 7. Our results suggest that trait sampling for many objectives in species-rich plant communities may require the considerable effort of sampling at least one individual of each species in each plot, and that investment in complete sampling, though great, may be worthwhile for at least some traits.},
-author = {Baraloto, Christopher and Paine, C. E. Timothy and Pati{\~{n}}o, Sandra and Bonal, Damien and H{\'{e}}rault, Bruno and Chave, J{\'{e}}r{\^{o}}me},
-doi = {10.1111/j.1365-2435.2009.01600.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baraloto et al. - 2010 - Functional trait variation and sampling strategies in species rich plant communities.pdf:pdf},
-journal = {Functional Ecology},
-number = {1},
-pages = {208--216},
-title = {{Functional trait variation and sampling strategies in species rich plant communities}},
-url = {http://doi.wiley.com/10.1111/j.1365-2435.2009.01600.x},
-volume = {24},
-year = {2010}
-}
-@article{TerSteege2013,
-abstract = {The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4{\%}) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species—less diverse than the North American tree flora—accounts for half of the world's most diverse tree community.},
-annote = {10.1126/science.1243092},
-author = {ter Steege, Hans and Pitman, Nigel C. A. and Sabatier, Daniel and Baraloto, Christopher and Salom{\~{a}}o, Rafael P. and Guevara, Juan Ernesto and Phillips, Oliver L. and Castilho, Carolina V. and Magnusson, William E. and Molino, Jean-Fran{\c{c}}ois and Monteagudo, Abel and {N{\'{u}}{\~{n}}ez Vargas}, Percy and Montero, Juan Carlos and Feldpausch, Ted R. and Coronado, Eur{\'{i}}dice N. Honorio and Killeen, Tim J. and Mostacedo, Bonifacio and Vasquez, Rodolfo and Assis, Rafael L. and Terborgh, John and Wittmann, Florian and Andrade, Ana C. S. and Laurance, William F. and Laurance, Susan G. W. and Marimon, Beatriz Schwantes and Marimon, Ben-Hur and {Guimar{\~{a}}es Vieira}, Ima C{\'{e}}lia and Amaral, I{\^{e}}da Le{\~{a}}o and Brienen, Roel and Castellanos, Hern{\'{a}}n and {C{\'{a}}rdenas L{\'{o}}pez}, Dairon and Duivenvoorden, Joost F. and Mogoll{\'{o}}n, Hugo F. and Matos, Francisca Dion{\'{i}}zia de Almeida and D{\'{a}}vila, N{\'{a}}llarett and Garc{\'{i}}a-Villacorta, Roosevelt and {Stevenson Diaz}, Pablo Roberto and Costa, Fl{\'{a}}via and Emilio, Thaise and Levis, Carolina and Schietti, Juliana and Souza, Priscila and Alonso, Alfonso and Dallmeier, Francisco and Montoya, Alvaro Javier Duque and {Fernandez Piedade}, Maria Teresa and Araujo-Murakami, Alejandro and Arroyo, Luzmila and Gribel, Rogerio and Fine, Paul V. A. and Peres, Carlos A. and Toledo, Marisol and Aymard, Gerardo A. and Baker, Tim and Cer{\'{o}}n, Carlos and Engel, Julien and Henkel, Terry W. and Maas, Paul and Petronelli, Pascal and Stropp, Juliana and Zartman, Charles Eugene and Daly, Doug and Neill, David and Silveira, Marcos and Paredes, Marcos R{\'{i}}os and Chave, J{\'{e}}r{\^{o}}me and {Lima Filho}, Di{\'{o}}genes de Andrade and J{\o}rgensen, Peter M{\o}ller and Fuentes, Alfredo and Sch{\"{o}}ngart, Jochen and {Cornejo Valverde}, Fernando and {Di Fiore}, Anthony and Jimenez, Eliana M. and Pe{\~{n}}uela-Mora, Maria Cristina and Phillips, Juan Fernando and Rivas, Gonzalo and van Andel, Tinde R. and von Hildebrand, Patricio and Hoffman, Bruce and Zent, Egl{\'{e}}e L. and Malhi, Yadvinder and Prieto, Adriana and Rudas, Agust{\'{i}}n and Ruschell, Ademir R. and Silva, Natalino and Vos, Vincent and Zent, Stanford and Oliveira, Alexandre A. and Schutz, Angela Cano and Gonzales, Therany and {Trindade Nascimento}, Marcelo and Ramirez-Angulo, Hirma and Sierra, Rodrigo and Tirado, Milton and {Uma{\~{n}}a Medina}, Mar{\'{i}}a Natalia and van der Heijden, Geertje and Vela, C{\'{e}}sar I. A. and {Vilanova Torre}, Emilio and Vriesendorp, Corine and Wang, Ophelia and Young, Kenneth R. and Baider, Claudia and Balslev, Henrik and Ferreira, Cid and Mesones, Italo and Torres-Lezama, Armando and {Urrego Giraldo}, Ligia Estela and Zagt, Roderick and Alexiades, Miguel N. and Hernandez, Lionel and Huamantupa-Chuquimaco, Isau and Milliken, William and {Palacios Cuenca}, Walter and Pauletto, Daniela and {Valderrama Sandoval}, Elvis and {Valenzuela Gamarra}, Luis and Dexter, Kyle G. and Feeley, Kenneth J. and Lopez-Gonzalez, Gabriela and Silman, Miles R.},
-doi = {10.1126/science.1243092},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/ter Steege et al. - 2013 - Hyperdominance in the Amazonian Tree Flora.pdf:pdf},
-journal = {Science},
-number = {6156},
-pages = {1243092},
-title = {{Hyperdominance in the Amazonian Tree Flora}},
-url = {http://www.sciencemag.org/content/342/6156/1243092.abstract},
-volume = {342},
-year = {2013}
-}
-@misc{INRA2008,
-author = {INRA},
-title = {{Charte utilisateur pour l'usage des ressources informatiques de l'INRA}},
-url = {https://www.inra.fr/internet/Projets/charte-informatique/charte.pdf},
-year = {2008}
-}
-@article{Veech2014,
-abstract = {The analysis of species co-occurrence patterns continues to be a main pursuit of ecologists, primarily because the coexistence of species is fundamentally important in evaluating various theories, principles and concepts. Examples include community assembly, equilibrium versus non-equilibrium organization of communities, resource partitioning and ecological character displacement, the local–regional species diversity relationship, and the metacommunity concept. Traditionally, co-occurrence has been measured and tested at the level of an entire species presence–absence matrix wherein various algorithms are used to randomize matrices and produce statistical null distributions of metrics that quantify structure in the matrix. This approach implicitly recognizes a presence– absence matrix as having some real ecological identity (e.g. a set of species exhibiting nestedness among a set of islands) in addition to being a unit of statistical analysis. An emerging alternative is to test for non-random co-occurrence between paired species. The pairwise approach does not analyse matrix-level structure and thus views a species pair as the fundamental unit of co-occurrence. Inferring process from pattern is very difficult in analyses of co-occurrence; however, the pairwise approach may make this task easier by simplifying the analysis and resulting inferences to associations between paired species.},
-author = {Veech, Joseph A.},
-doi = {10.1111/jbi.12318},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veech - 2014 - The pairwise approach to analysing species co-occurrence.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {6},
-pages = {1029--1035},
-title = {{The pairwise approach to analysing species co-occurrence}},
-url = {http://doi.wiley.com/10.1111/jbi.12318},
-volume = {41},
-year = {2014}
-}
-@article{Fukami2005,
-abstract = {Despite decades of research, it remains controversial whether ecological communities converge towards a common structure determined by environmental conditions irrespective of assembly history. Here, we show experimentally that the answer depends on the level of community organization considered. In a 9-year grassland experiment, we manipulated initial plant composition on abandoned arable land and subsequently allowed natural colonization. Initial compositional variation caused plant communities to remain divergent in species identities, even though these same communities converged strongly in species traits. This contrast between species divergence and trait convergence could not be explained by dispersal limitation or community neutrality alone. Our results show that the simultaneous operation of trait-based assembly rules and species-level priority effects drives community assembly, making it both deterministic and historically contingent, but at different levels of community organization.},
-author = {Fukami, Tadashi and Bezemer, T. Martijn and Mortimer, Simon R. and {Van Der Putten}, Wim H.},
-doi = {10.1111/j.1461-0248.2005.00829.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fukami et al. - 2005 - Species divergence and trait convergence in experimental plant community assembly.pdf:pdf},
-journal = {Ecology Letters},
-number = {12},
-pages = {1283--1290},
-title = {{Species divergence and trait convergence in experimental plant community assembly}},
-volume = {8},
-year = {2005}
-}
-@article{Reilly2002,
-abstract = {Here we investigate the clustering of simian immunodeficiency virus (SIV)-infected cells in a lymphatic tissue sample taken from a rhesus macaque to test a spatial proximity model of the spread of infection. We see that standard methods for analysis of the clustering of point processes are not entirely satisfactory for this application, so we define a novel statistic to understand the clustering in the data. This statistic examines how events spread out from certain points deemed cluster centers. Using this statistic, we can demonstrate the statistical significance of the clustering and examine over what distances this clustering is witnessed. We use Bayesian methods to fully assess the uncertainty in the estimation of this statistic by positing a model for the process. (We assume the process is a nonhomogeneous Poisson process with an intensity that is a linear combination of Gaussian densities.) We see that the distances at which clustering is present are consistent with a simple model of SIV spread within the lymph node.},
-annote = {Article
-English
-J AMER STATIST ASSN
-632TX},
-author = {Reilly, C. and Schacker, T. and Haase, A. T. and Wietgrefe, S. and Krason, D.},
-doi = {10.1198/016214502388618735},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reilly et al. - 2002 - The clustering of infected SIV cells in lymphatic tissue.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {460},
-pages = {943--954},
-title = {{The clustering of infected SIV cells in lymphatic tissue}},
-url = {http://www.tandfonline.com/doi/abs/10.1198/016214502388618735},
-volume = {97},
-year = {2002}
-}
-@article{Ricotta2006,
-abstract = {Weikard et al. (Diversity and Distributions, 12, 215-217) show that the taxonomic diversity measure proposed by Ricotta (2004) violates 'weak species monotonicity'. This condition requires that the addition of a species to a given species set should always increase diversity if abundances change only marginally. They further propose a new taxonomic diversity index that overcomes this drawback. In this paper, some statistical properties of this new diversity index are briefly analysed.},
-annote = {Cited By (since 1996):3
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: DIDIF
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo},
-doi = {10.1111/j.1366-9516.2005.00233.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2006 - Strong requirements for weak diversities.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {2},
-pages = {218--219},
-title = {{Strong requirements for weak diversities}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33644836545{\&}partnerID=40{\&}md5=7c03fa3603b0e02ce494fcab7452a049},
-volume = {12},
-year = {2006}
-}
-@article{Kim1995,
-abstract = {This paper presents evidence on the long-run trends in U. S. regional specialization and localization and examines which model of regional specialization is most consistent with the data. Regional specialization in the United States rose substantially between 1860 and the turn of the twentieth century, flattened out during the interwar years, and then fell substantially and continuously since the 1930s. The analysis of the long-run trends in U. S. regional specialization and localization supports explanations based on production scale economies and the Heckscher-Ohlin model but is inconsistent with explanations based on external economies.},
-author = {Kim, Sukkoo},
-doi = {10.2307/2946643},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kim - 1995 - Expansion of Markets and the Geographic Distribution of Economic Activities The Trends in U.S. Regional Manufacturing Struc.pdf:pdf},
-journal = {The Quarterly Journal of Economics},
-number = {4},
-pages = {881--908},
-title = {{Expansion of Markets and the Geographic Distribution of Economic Activities: The Trends in U.S. Regional Manufacturing Structure, 1860-1987}},
-url = {https://academic.oup.com/qje/article-abstract/110/4/881/1870549/Expansion-of-Markets-and-the-Geographic},
-volume = {110},
-year = {1995}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2004,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n°2004-1307 du 26 novembre 2004 modifiant le d{\'{e}}cret n° 2000-815 du 25 ao{\^{u}}t 2000 relatif {\`{a}} l'am{\'{e}}nagement et {\`{a}} la r{\'{e}}duction du temps de travail dans la fonction publique de l'Etat.}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000258249},
-year = {2004}
-}
-@article{Ulanowicz2001,
-abstract = {The application of information theory (IT) to ecology has occurred along two separate lines: (1) it has been used to quantify the distribution of stocks and numbers of organisms; and (2) it has been employed to quantify the pattern of interactions of trophic processes. By and large, the first endeavor has resulted in relatively few insights into ecosystem dynamics and has generated much ambiguity and disappointment, so that most ecologists remain highly skeptical about the advisability of applying IT to ecology. By contrast, the second, and less well-known application has shed light on the possibility that ecosystem behavior is the most palpable example of a purely natural [`]infodynamics' that transcends classical dynamics, but remains well within the realm of quantitative description.},
-annote = {doi: DOI: 10.1016/S0097-8485(01)00073-0},
-author = {Ulanowicz, Robert E.},
-doi = {10.1016/S0097-8485(01)00073-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ulanowicz - 2001 - Information theory in ecology.pdf:pdf},
-journal = {Computers {\&} Chemistry},
-number = {4},
-pages = {393--399},
-title = {{Information theory in ecology}},
-url = {http://www.sciencedirect.com/science/article/B6TFV-43MBTJS-7/2/7c27b72dca1f1853cfb0a61797a76cbe},
-volume = {25},
-year = {2001}
-}
-@article{Wardle1997,
-abstract = {Island area is frequently a major determinant of the species composition of biological communities; community structure, in turn, often has important effects on ecosystem-level properties. Fifty islands of varying area were selected in an archipelago in the northern Swedish boreal forest zone, in which larger islands bum more frequently than smaller ones through wildfire arising from lightning strike, thus inducing a significant relationship between island area and plant species composition. This relationship was found to be a major factor in determining several ecosystem-level properties of these islands, including standing biomass, plant litter decomposition, nitrogen mineralization, terrestrial carbon partitioning, humus accumulation, and plant nitrogen acquisition.},
-author = {Wardle, David A. and Zackrisson, Olle and H{\"{o}}rnberg, Greger and Gallet, Christiane},
-doi = {10.1126/science.277.5330.1296},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wardle et al. - 1997 - The Influence of Island Area on Ecosystem Properties.pdf:pdf},
-journal = {Science},
-number = {5330},
-pages = {1296--1299},
-title = {{The Influence of Island Area on Ecosystem Properties}},
-url = {http://science.sciencemag.org/content/277/5330/1296},
-volume = {277},
-year = {1997}
-}
-@article{Herault2011,
-abstract = {1. Functional traits are posited to explain interspecific differences in performance, but these relationships are difficult to describe for long-lived organisms such as trees, which exhibit strong ontogenetic changes in demographic rates. Here, we use a size-dependent model of tree growth to test the extent to which of 17 functional traits related to leaf and stem economics, adult stature and seed size predict the ontogenetic trajectory of tree growth. 2. We used a Bayesian modelling framework to parameterize and contrast three size-dependent diameter growth models using 16 years of census data from 5524 individuals of 50 rain forest tree species: a size-dependent model, a size-dependent model with species-specific parameters and a size-dependent model based on functional traits. 3. Most species showed clear hump-shaped ontogenetic growth trajectories and, across species, maximum growth rate varied nearly tenfold, from 0.58 to 5.51 mm year−1. Most species attained their maximum growth at 60{\%} of their maximum size, whereas the magnitude of ontogenetic changes in growth rate varied widely among species. 4. The Trait-Model provided the best compromise between explained variance and model parsimony and needed considerably fewer parameters than the model with species terms. 5. Stem economics and adult stature largely explained interspecific differences in growth strategy. Maximum absolute diameter growth rates increased with increasing adult stature and leaf $\delta$13C and decreased with increasing wood density. Species with light wood had the greatest potential to modulate their growth, resulting in hump-shaped ontogenetic growth curves. Seed size and leaf economics, generally thought to be of paramount importance for plant performance, had no significant relationships with the growth parameters. 6. Synthesis. Our modelling approach offers a promising way to link demographic parameters to their functional determinants and hence to predict growth trajectories in species-rich communities with little parameter inflation, bridging the gap between functional ecology and population demography.},
-author = {H{\'{e}}rault, Bruno and Bachelot, B{\'{e}}n{\'{e}}dicte and Poorter, Lourens and Rossi, Vivien and Bongers, Frans and Chave, J{\'{e}}r{\^{o}}me and Paine, C. E. Timothy and Wagner, Fabien and Baraloto, Christopher},
-doi = {10.1111/j.1365-2745.2011.01883.x},
-file = {::},
-journal = {Journal of Ecology},
-number = {6},
-pages = {1431--1440},
-title = {{Functional traits shape ontogenetic growth trajectories of rain forest tree species}},
-url = {http://doi.wiley.com/10.1111/j.1365-2745.2011.01883.x},
-volume = {99},
-year = {2011}
-}
-@article{Diggle1985b,
-author = {Diggle, Peter J. and Gates, David J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle, Gates - 1985 - Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina Comment.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {392},
-pages = {813},
-title = {{Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina: Comment}},
-volume = {80},
-year = {1985}
-}
-@article{Devereux1998,
-abstract = {This paper considers the factors that influence the locational decisions of multinational firms. A model in which firms produce differentiated products in imperfectly competitive markets is developed, in the spirit of Horstmann and Markusen (1992). Firms choose between a number of foreign locations; the outside options of exporting to or not serving the foreign market are explicitly modelled. Particular attention is paid to the impact of profit taxes; the separate roles of effective average and marginal tax rates are identified. The model is applied to a panel of US firms locating in the European market. Agglomeration effects are found to be important. The effective average tax rate plays a role in the choice between locations, but not in the choice of whether to locate production in Europe compared with one of the outside options.},
-author = {Devereux, Michael P. and Griffith, Rachel},
-doi = {10.1016/S0047-2727(98)00014-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Devereux, Griffith - 1998 - Taxes and the location of production evidence from panel of US multinationals.pdf:pdf},
-journal = {Journal of Public Economics},
-number = {3},
-pages = {335--367},
-title = {{Taxes and the location of production : evidence from panel of US multinationals}},
-url = {http://www.sciencedirect.com/science/article/pii/S0047272798000140},
-volume = {68},
-year = {1998}
-}
-@article{Carvalho2013,
-abstract = {Beta diversity and nestedness are central concepts of ecology and biogeography and evaluation of their relationships is in the focus of contemporary ecological and conservation research. Beta diversity patterns are originated from two distinct processes: the replacement (or turnover) of species and the loss (or gain) of species leading to richness differences. Nested distributional patterns are generally thought to have a component deriving from beta diversity which is independent of replacement processes. Quantification of these phenomena is often made by calculating a measure of beta diversity, and the resulting value being subsequently partitioned into a contribution by species replacement plus a fraction shared by beta diversity and nestedness. Three methods have been recently proposed for such partitioning, all of them based on pairwise comparisons of sites. In this paper, the performance of these methods was evaluated on theoretical grounds and tested by a simulation study in which different gradients of dissimilarity, with known degrees of species replacement and species loss, were created. Performance was also tested using empirical data addressing land-use induced changes in endemic arthropod communities of the Terceira Island in the Azores. We found that the partitioning of $\beta$cc (dissimilarity in terms of the Jaccard index) into two additive fractions, $\beta$-3 (dissimilarity due to species replacement) plus $\beta$rich (dissimilarity due to richness differences) reflects the species replacement and species loss processes across the simulated gradients in an ecologically and mathematically meaningful way, whilst the other two methods lack mathematical consistency and prove conceptually self-contradictory. Moreover, the first method identified a selective local extinction process for endemic arthropods, triggered by land-use changes, while the latter two methods overweighted the replacement component and led to false conclusions. Their basic flaw derives from the fact that the proposed replacement and nestedness components (deemed to account for species loss) are not scaled in the same way as the measure that accounts for the total dissimilarity (S{\o}rensen and Jaccard indices). We therefore recommend the use of $\beta$cc=$\beta$-3+$\beta$rich, since its components are scaled in the same units and their responses are proportional to the replacement and the gain/loss of species.},
-author = {Carvalho, Jos{\'{e}} C. and Cardoso, Pedro and Borges, Paulo A. V. and Schmera, D{\'{e}}nes and Podani, J{\'{a}}nos},
-doi = {10.1111/j.1600-0706.2012.20980.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Carvalho et al. - 2013 - Measuring fractions of beta diversity and their relationships to nestedness a theoretical and empirical compari.pdf:pdf},
-journal = {Oikos},
-number = {6},
-pages = {825--834},
-title = {{Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches}},
-url = {http://doi.wiley.com/10.1111/j.1600-0706.2012.20980.x},
-volume = {122},
-year = {2013}
-}
-@book{Legendre2012,
-author = {Legendre, Pierre and Legendre, Louis},
-edition = {3rd Ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Legendre - 2012 - Numerical Ecology.pdf:pdf},
-isbn = {978-0-444-53868-0},
-publisher = {Elsevier},
-title = {{Numerical Ecology}},
-year = {2012}
-}
-@article{Cowell1981a,
-author = {Cowell, Frank A. and Kuga, Kiyoshi},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cowell, Kuga - 1981 - Additivity and the entropy concept An axiomatic approach to inequality measurement.pdf:pdf},
-journal = {Journal of Economic Theory},
-number = {1},
-pages = {131--143},
-title = {{Additivity and the entropy concept: An axiomatic approach to inequality measurement}},
-url = {http://www.sciencedirect.com/science/article/B6WJ3-4CYGB9D-GV/2/bd3ca70baf3dc490b26f564953f6b830},
-volume = {25},
-year = {1981}
-}
-@article{Baddeley1993,
-abstract = {Techniques for analysing three-dimensional spatial point patterns are demonstrated on data from a confocal microscope recording the locations of cells in three dimensions. New computational techniques are proposed for edge corrections and empty space measurement. A novel feature of the data is replication and nesting in a sampling design: multiple spatial patterns were observed from each of several animals. For this we develop a ratio regression approach.},
-author = {Baddeley, Adrian J. and Moyeed, R. A. and Howard, C. V. and Boyde, A.},
-doi = {10.2307/2986181},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley et al. - 1993 - Analysis of a Three-Dimensional Point Pattern with Replication.pdf:pdf},
-journal = {Applied Statistics},
-number = {4},
-pages = {641--668},
-title = {{Analysis of a Three-Dimensional Point Pattern with Replication}},
-url = {https://www.jstor.org/stable/2986181},
-volume = {42},
-year = {1993}
-}
-@article{Chalmandrier2014,
-author = {Chalmandrier, Lo{\"{i}}c and M{\"{u}}nkem{\"{u}}ller, Tamara and Devictor, Vincent and Lavergne, S{\'{e}}bastien and Thuiller, Wilfried},
-doi = {10.1111/2041-210X.12297},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chalmandrier et al. - 2015 - Decomposing changes in phylogenetic and functional diversity over space and time.pdf:pdf},
-issn = {2041210X},
-journal = {Methods in Ecology and Evolution},
-month = {oct},
-number = {1},
-pages = {109--118},
-title = {{Decomposing changes in phylogenetic and functional diversity over space and time}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12297},
-volume = {6},
-year = {2015}
-}
-@unpublished{Ottaviano2004a,
-abstract = {What are the economic consequences to U.S. natives of the growing diversity of American cities? Is their productivity or utility affected by cultural diversity as measured by diversity of countries of birth of U.S. residents? We document in this paper a very robust correlation: US-born citizens living in metropolitan areas where the share of foreign-born increased between 1970 and 1990, experienced a significant increase in their wage and in the rental price of their housing. Such finding is economically significant and survives omitted variable bias and endogeneity bias. As people and firms are mobile across cities in the long run we argue that, in equilibrium, these correlations are consistent only with a net positive effect of cultural diversity on productivity of natives.},
-author = {Ottaviano, Gianmarco I P and Peri, Giovanni},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ottaviano, Peri - 2004 - The economic value of cultural diversity evidence from us cities.pdf:pdf},
-series = {NBER Working Paper},
-title = {{The economic value of cultural diversity: evidence from us cities}},
-url = {http://www.nber.org/papers/w10904{\%}0ANATIONAL},
-year = {2004}
-}
-@article{OhUallachain2007,
-abstract = {Recent research shows growing concentration of corporate decision-making functions in metropolitan cores and strong relationships between managerial activities and producer services. The paper investigates the location of 12 disaggregated producer service sectors in Phoenix, Arizona. Concentration of legal, accounting and computer services underpin the economy of the inner core. Second-order unweighted and employment-weighted distance-based clustering of establishments in each sector are calculated. Clustering of legal establishments is particularly high and there is a consistent pattern of higher clustering levels among the larger establishments of most sectors. Establishment size in several sectors is inversely related to distance from the centre. These results are interpreted as evidence that large establishments are drawn to central locations to exploit information externalities. Concentration in the inner core, clustering and the sensitivity of establishment size to distance from the CBD are significantly correlated.},
-author = {{\'{O}} hUallach{\'{a}}in, Breandan and Leslie, Timothy F},
-doi = {10.1080/00420980701373453},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/{\'{O}} hUallach{\'{a}}in, Leslie - 2007 - Producer Services in the Urban Core and Suburbs of Phoenix, Arizona.pdf:pdf},
-journal = {Urban Studies},
-number = {8},
-pages = {1581--1601},
-title = {{Producer Services in the Urban Core and Suburbs of Phoenix, Arizona}},
-url = {http://usj.sagepub.com/content/44/8/1581.abstract},
-volume = {44},
-year = {2007}
-}
-@article{Galiano1987,
-abstract = {(1) A Monte-Carlo test for spatial pattern in vegetation is presented, based on the random permutation of original abundance data recorded in belt transects. Monte-Carlo simulation allows the testing of null hypotheses and the estimation of confidence intervals for any previously defined pattern analysis statistics. (2) The test was applied with Hill's local variance and Galiano's new local variance analyses to six artificial sets of data and to data from Spanish oligotrophic grasslands in three different stages of ecological succession. (3) Results from the artificial data indicate that the method is capable of providing accurate information concerning dimensions and densities of species clumps. (4) Preliminary results from real data suggested the disappearance of pattern during successional time in those species remaining in the community.},
-author = {Galiano, E. F. and Castro, I. and Sterling, A.},
-doi = {10.2307/2260303},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Galiano, Castro, Sterling - 1987 - A Test for Spatial Pattern in Vegetation Using a Monte-Carlo Simulation.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {915--924},
-title = {{A Test for Spatial Pattern in Vegetation Using a Monte-Carlo Simulation}},
-url = {https://www.jstor.org/stable/2260303},
-volume = {75},
-year = {1987}
-}
-@book{Boggan1997,
-address = {Washington, D.C.},
-author = {Boggan, J. and Funk, V. and Kelloff, C. and Hoff, M. and Cremers, G. and Feuillet, C.},
-edition = {2nd ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Boggan et al. - 1997 - Checklist of the Plants of the Guianas.pdf:pdf},
-publisher = {Museum of Natural History, Smithsonian Institution},
-title = {{Checklist of the Plants of the Guianas}},
-url = {http://www.mnh.si.edu/biodiversity/bdg/checklst.html},
-year = {1997}
-}
-@article{Diaz2003,
-abstract = {The dominant protocol to study the effects of plant diversity on ecosystem functioning has involved synthetically assembled communities, in which the experimental design determines species composition. By contrast, the composition of naturally assembled communities is determined by environmental filters, species recruitment and dispersal, and other assembly processes. Consequently, natural communities and ecosystems can differ from synthetic systems in their reaction to changes in diversity. Removal experiments, in which the diversity of naturally assembled communities is manipulated by removing various components, complement synthetic-assemblage experiments in exploring the relationship between diversity and ecosystem functioning. Results of recent removal experiments suggest that they are more useful for understanding the ecosystem effects of local, nonrandom extinctions, changes in the natural abundance of species, and complex interspecific interactions. This makes removal experiments a promising avenue for progress in ecological theory and an important source of information for those involved in making land-use and conservation decisions.},
-author = {D{\'{i}}az, Sandra and Symstad, A .J. and Chapin, F. Stuart III and Wardle, David A. and Huenneke, L. F.},
-doi = {10.1016/S0169-5347(03)00007-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diaz et al. - 2003 - Functional diversity revealed by removal experiments.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {3},
-pages = {140--146},
-title = {{Functional diversity revealed by removal experiments}},
-volume = {18},
-year = {2003}
-}
-@article{Bellier2012,
-abstract = {We introduce a novel spatially explicit framework for decomposing species distributions into multiple scales from count data. These kinds of data are usually positively skewed, have non-normal distributions and are spatially autocorrelated. To analyse such data, we propose a hierarchical model that takes into account the observation process and explicitly deals with spatial autocorrelation. The latent variable is the product of a positive trend representing the non-constant mean of the species distribution and of a stationary positive spatial field representing the variance of the spatial density of the species distribution. Then, the different scales of emergent structures of the distribution of the population in space are modelled from the latent density of the species distribution using multi-scale variogram models. Multi-scale kriging is used to map the spatial patterns previously identified by the multi-scale models. We show how our framework yields robust and precise estimates of the relevant scales both for spatial count data simulated from well-defined models, and in a real case-study based on seabird count data (the common guillemot Uria aalge) provided by large-scale aerial surveys of the Bay of Biscay (France) performed over a winter. Our stochastic simulation study provides guidelines on the expected uncertainties of the scales estimates. Our results indicate that the spatial structure of the common guillemot can be modelled as a three-level hierarchical system composed of a very broad-scale pattern (similar to 200 km) with a stable location over time that might be environmentally controlled, a broad-scale pattern (similar to 50 km) with a variable shape and location, that might be related to shifts in prey distribution, and a fine-scale pattern (similar to 10 km) with a rather stable shape and location, that might be controlled by behavioural processes. Our framework enables the development of robust, scale-dependent hypotheses regarding the potential ecological processes that control species distributions.},
-annote = {ISI Document Delivery No.: 967XP
-Times Cited: 0
-Cited Reference Count: 77
-Bellier, Edwige Monestiez, Pascal Certain, Gregoire Chadoeuf, Joel Bretagnolle, Vincent
-French Government (MEDD); Univ. of La Rochelle; Communaute de Commune de La Rochelle; Provence Alpes Cotes d'Azur province; Inst. National pour la Recherche Agronomique (INRA); Norwegian Research Council (NRC)
-We wish to thank the two observers, Rodolphe Bernard and Thibault Dieuleveult, for their dedicated field work via aircraft in 2001-2002. Flight schedules and logistics were organised by Sylvie Houte (CNRS). This program was funded by the French Government (MEDD). We thank Michel Metais and LPO, who led the program. GC received a grant from Univ. of La Rochelle and the Communaute de Commune de La Rochelle. EB was supported by the Provence Alpes Cotes d'Azur province and by the Inst. National pour la Recherche Agronomique (INRA) and in the final stage of the project, by the Norwegian Research Council (NRC). We are very grateful for valuable comments of several reviewers on earlier version of this manuscript and we wish to thank M. J. Anderson for her very relevant comments in the final stage of the manuscript. We thank Richard Hedger and Marianne Rambeaud for their help in proofreading the English of the manuscript in its final stage.
-Wiley-blackwell
-Hoboken},
-author = {Bellier, E. and Monestiez, P. and Certain, G. and Chadoeuf, Jo{\"{e}}l and Bretagnolle, V.},
-doi = {10.1111/j.1600-0587.2011.06456.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bellier et al. - 2012 - Decomposing the heterogeneity of species distributions into multiple scales a hierarchical framework for large-s.pdf:pdf},
-journal = {Ecography},
-number = {9},
-pages = {839--854},
-title = {{Decomposing the heterogeneity of species distributions into multiple scales: a hierarchical framework for large-scale count surveys}},
-volume = {35},
-year = {2012}
-}
-@article{Scheiner2011,
-abstract = {Various ecological mechanisms influence the forms of species richness relationships (SRRs). These mechanisms can be gathered under five general categories: more individuals, environmental heterogeneity, dispersal limitations, biotic interactions, and multiple species pools. Often only the first two categories are discussed. In contrast, we examine all five and explore how they can influence the form of SRRs. We discuss how various sampling schemes and methods of SRR construction can be used to gain insight about how various processes influence species richness patterns. The field is ripe for probing these effects through more complex simulation models or more sophisticated mathematical approaches. To facilitate deeper understanding, we need to embrace the full spectrum of SRRs and reconsider the assumed common knowledge about the functional form of SRRs. The relationship between species richness and the space or time over which it is sampled has received increasing attention over the past decade, resulting in extensive debates about terminology and methods of construction. These debates reflect deep conceptual issues; to resolve them we discuss the long history of species richness relationships (SRRs) and the connections among different methodological and terminological approaches. We reinforce recent calls to organize the variety of methods used to construct SRRs into a cohesive structure. SRRs are descriptors of various aspects of inventory (alpha-and gamma-) diversity and the various types of SRRs serve different purposes. Contrary to most claims, SRRs do not provide a direct measure of differentiation (beta-) diversity.},
-author = {Scheiner, Samuel M. and Chiarucci, Alessandro and Fox, Gordon A. and Helmus, Matthew R. and McGlinn, Daniel J. and Willig, Michael R.},
-doi = {10.1890/10-1426.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheiner et al. - 2011 - The underpinnings of the relationship of species richness with space and time.pdf:pdf},
-journal = {Ecological Monographs},
-number = {2},
-pages = {195--213},
-title = {{The underpinnings of the relationship of species richness with space and time}},
-volume = {81},
-year = {2011}
-}
-@article{Dobson2001,
-abstract = {Ceara Rise, located east the Amazon River mouth, is covered with a thick blanket of pelagic carbonate and hemipelagic terrigenous sediment. The terrigenous component has been extracted from 57 bulk sediment samples at Ocean Drilling Program (ODP) Sites 925 and 929 on Ceara Rise to obtain a Cenozoic record of riverine discharge from northern South America. From the early Eocene to early Miocene (55-20 Ma), terrigenous accumulation was dominated by moderate amounts of generally large-grained, gray to green sediment especially depleted in elements that are enriched in post-Archaean shale (e.g. Cs, Th, Yb). However, pulsed inputs of relatively small-grained, gray to green terrigenous sediment less depleted in the above elements occurred in the late Eocene and Oligocene. The accumulation of terrigenous sediment decreased significantly until 16.5 Ma. In the middle Miocene (16.5-13 Ma), terrigenous accumulation was dominated by small amounts of small-grained, tan sediment notably depleted in Na and heavy rare earth elements. The accumulation rate of terrigenous sediment increased markedly from the latest Miocene (10 Ma) to the present day, a change characterized by deposition of gray-green sediment enriched in elements that are enriched in post-Archaean shale. Observed changes in terrigenous sediment at Ceara Rise record tectonism and erosion in northern South America. The Brazil and Guyana shields supplied sediment to the eastern South American margin until the middle Miocene (20-16.5 Ma) when a period of thrusting, shortening and uplift changed the source region, probably first to highly weathered and proximal Phanerozoic sediments. By the late Miocene (9 Ma), there was a transcontinental connection between the Andes and eastern South America. Weathering products derived from the Andes have increasingly dominated terrigenous deposition at Ceara Rise since the Late Miocene and especially since the late Pliocene. {\textcopyright} 2001 Elsevier Science B.V.},
-author = {Dobson, David M. and Dickens, Gerald R. and Rea, David K.},
-doi = {10.1016/S0031-0182(00)00161-9},
-journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
-number = {3-4},
-pages = {215--229},
-title = {{Terrigenous sediment on Ceara Rise: A Cenozoic record of South American orogeny and erosion}},
-volume = {165},
-year = {2001}
-}
-@article{Baddeley2011a,
-abstract = {We develop new tools for formal inference and informal model validation in the analysis of spatial point pattern data. The score test is gen- eralized to a “pseudo-score” test derived from Besag's pseudo-likelihood, and to a class of diagnostics based on point process residuals. The results lend theoretical support to the established practice of using functional sum- mary statistics, such as Ripley's K-function, when testing for complete spa- tial randomness; and they provide new tools such as the compensator of the K-function for testing other fitted models. The results also support localiza- tion methods such as the scan statistic and smoothed residual plots. Software for computing the diagnostics is provided.},
-author = {Baddeley, Adrian J. and Rubak, Ege and M{\o}ller, Jesper},
-doi = {10.1214/11-STS367},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, Rubak, M{\o}ller - 2011 - Score, Pseudo-Score and Residual Diagnostics for Spatial Point Process Models.pdf:pdf},
-journal = {Statistical Science},
-number = {4},
-pages = {613--646},
-title = {{Score, Pseudo-Score and Residual Diagnostics for Spatial Point Process Models}},
-url = {http://projecteuclid.org/euclid.ss/1330437942},
-volume = {26},
-year = {2011}
-}
-@article{Anderson1992,
-abstract = {Access to markets and raw materials is nearly always mentioned in industrial location studies as an important locational factor. This article demonstrates a methodological approach based on inter-industry linkages and using secondary data to identify target industries for economic development initiatives. In this application we characterize Alabama's industrial base, identify industries with strong forward and backward linkages to base Alabama industries, and highlight a subset of especially good prospects.},
-author = {Anderson, Donald and Johnston, Stephen A.},
-doi = {10.1111/j.1468-2257.1992.tb00937.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anderson, Johnston - 1992 - A Linkage Approach to Industrial Location.pdf:pdf},
-journal = {Growth and Change},
-number = {3},
-pages = {321--334},
-title = {{A Linkage Approach to Industrial Location}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1468-2257.1992.tb00937.x/abstract},
-volume = {23},
-year = {1992}
-}
-@article{Chao2014b,
-abstract = {1. Traditional species diversity measures do notmake distinctions among species. Faith's phylogenetic diversity (PD), which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species, takes into account phylogenetic differences among species and has found many applications in various research fields. In this paper, we extend Faith's PD to represent the total length of a phylogenetic tree from any fixed point on its main trunk. 2. Like species richness, Faith's PD tendstobeanincreasingfunction of sampling effort and thus tends to increase with sample completeness.We develop in this paper the ‘PD accumulation curve' (an extension of the species accumulation curve) to depict howPDincreaseswith sampling size and sample completeness. 3. To make fair comparisons of Faith's PD among several assemblages based on sampling data from each assemblage, we derive both theoretical formulae and analytic estimators for seamless rarefaction (interpolation) and extrapolation (prediction).We develop a lower bound of the undetected PD for an incomplete sample to guide the extrapolation; the PD estimator for an extrapolated sample is generally reliable up to twice the size of the empirical sample. 4. We propose an integrated curve that smoothly links rarefaction and extrapolation to standardize samples on the basis of sample size or sample completeness. A bootstrap method is used to obtain the unconditional vari- ances ofPDestimators and to construct the confidence interval of the expectedPDfor a fixed sample size or fixed degree of sample completeness.This facilitates comparison of multiple assemblages of both rarefied and extrapo- lated samples. 5. Weillustrate our formulae and estimators using empirical data sets from Australian birds in two sites.We dis- cuss the extension of our approach to the case of multiple incidence data and to incorporate species abundances.},
-author = {Chao, Anne and Chiu, Chun-Huo and Hsieh, T. C. and Davis, Thomas and Nipperess, David A. and Faith, Daniel P.},
-doi = {10.1111/2041-210X.12247},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2015 - Rarefaction and extrapolation of phylogenetic diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {4},
-pages = {380--388},
-title = {{Rarefaction and extrapolation of phylogenetic diversity}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12247},
-volume = {6},
-year = {2015}
-}
-@article{Huisman2004,
-abstract = {In this article localization trends as a result of startups and closures are investigated in the Netherlands, using a distance-based approach. A major advantage of this method is that it does not suffer from aggregation bias that is inherent in area-based methods. This method controls for the existing spatial clustering of the industry. Plant openings and closures can either reinforce or weaken the existing localization pattern. We studied these localization tendencies for industries at the one-digit level. The major finding is that plant closures have a strong deconcentration effect, at the local as well as the regional level. Startups have a concentration effect at smaller spatial scales, but beyond 18 km this component also contributes to deconcentration. This result is in line with the spatial process of sprawl for most economic activities. However, results are different for economic sectors, and manufacturing clearly deviates from this general pattern, because it shows a localization trend except at the very small spatial level. Based on these results we do not find much support, except in the manufacturing industry, that industry dynamics in terms of new firm formation and closures, leads to stronger spatial agglomeration tendencies in the Netherlands.},
-author = {Huisman, Corina and van Wissen, Leo},
-doi = {10.1007/s00168-004-0196-7 Localization},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Huisman, van Wissen - 2004 - Localization effects of firm startups and closures in the Netherlands.pdf:pdf},
-journal = {The Annals of Regional Science},
-keywords = {Huisman (2004).pdf},
-mendeley-tags = {Huisman (2004).pdf},
-pages = {291--310},
-title = {{Localization effects of firm startups and closures in the Netherlands}},
-volume = {38},
-year = {2004}
-}
-@book{Braun-Blanquet1928,
-address = {Berlin},
-author = {Braun-Blanquet, Josias},
-booktitle = {Biologische studienb{\"{u}}cher},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Braun-Blanquet - 1928 - Pflanzensoziologie Grundz{\"{u}}ge der Vegetationskunde.pdf:pdf},
-publisher = {Springer},
-title = {{Pflanzensoziologie: Grundz{\"{u}}ge der Vegetationskunde}},
-year = {1928}
-}
-@article{Helmus2012,
-author = {Helmus, Matthew R. and Ives, Anthony R.},
-doi = {10.1890/11-0435.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Helmus, Ives - 2012 - Phylogenetic diversity–area curves.pdf:pdf},
-isbn = {0012-9658},
-journal = {Ecology},
-number = {sp8},
-pages = {S31--S43},
-publisher = {Ecological Society of America},
-title = {{Phylogenetic diversity–area curves}},
-url = {http://dx.doi.org/10.1890/11-0435.1},
-volume = {93},
-year = {2012}
-}
-@article{Arnan2015,
-abstract = {We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.},
-author = {Arnan, Xavier and Cerd{\'{a}}, Xim and Retana, Javier},
-doi = {10.7717/peerj.1241},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arnan, Cerd{\'{a}}, Retana - 2015 - Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, fu.pdf:pdf},
-journal = {PeerJ},
-pages = {e1241},
-title = {{Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants}},
-url = {https://peerj.com/articles/1241},
-volume = {3},
-year = {2015}
-}
-@article{Hey2001,
-abstract = {The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word ‘species'. The innumerable attacks on the problem have turned the often-repeated question ‘what are species?' into a philosophical conundrum. Today, the preferred form of attack is the well-crafted argument, and debaters seem to have stopped inquiring about what new information is needed to solve the problem. However, our knowledge is not complete and we have overlooked something. The species problem can be overcome if we understand our own role, as conflicted investigators, in causing the problem.},
-author = {Hey, Jody},
-doi = {10.1016/S0169-5347(01)02145-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hey - 2001 - The mind of the species problem.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {7},
-pages = {326--329},
-title = {{The mind of the species problem}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534701021450},
-volume = {16},
-year = {2001}
-}
-@article{Ward1999,
-abstract = {The development of distance-dependent growth and survival models depends on an understanding of the spatial distribution of the population in question. Ripley's L index (L-R) has found wide application for examining the spatial dispersion of plants. L-R is calculated as the square root of a weighted sum of the number of observed plant pairs that are less than a certain distance apart. The weighting used by L-R inflates the pair count sum to compensate for reduced pair counts for plants near the plot boundary. Using Monte Carlo simulations, we show that the variance in the observed number of tree pairs is not stabilized by the square root transformation at low expected counts. The non-linearity of the square root transformation introduces a consistent bias in both the first and second moments of the tree pair distribution. We present a derived estimator for Ripley's analytical L index (L-A) that provides a more accurate estimate of variance and mean. This new approach, based on a true Poisson variate, includes a modification of the previous edge correction method that incorporates a global estimate of mean pair density, rather than local values. This reduces variance caused by stochastic placement of point pairs near the boundary. Monte Carlo simulations verified the predictions of this model over a wide range of population sizes (25-1400). Simulation results showed that the L-R numerical estimate of the confidence limit was overly conservative by nearly a factor of two. The improved power and accuracy provided by L-A suggest that it would be fruitful to reexamine population spatial dispersion data in the literature using the analytical estimator (L-A). As an illustration, the power and accuracy of L-R and L-A to detect non-random spatial dispersions is compared using generated populations and six stands of mapped trees in Connecticut.},
-annote = {Article
-English
-ECOL MODEL
-196HD},
-author = {Ward, Jeffrey S and Ferrandino, Francis J},
-journal = {Ecological Modelling},
-number = {2-3},
-pages = {225--236},
-title = {{New derivation reduces bias and increases power of Ripley's L index}},
-volume = {116},
-year = {1999}
-}
-@article{Kricher2011,
-abstract = {"This full-color illustrated textbook offers the first comprehensive introduction to all major aspects of tropical ecology. It explains why the world's tropical rain forests are so universally rich in species, what factors may contribute to high species richness, how nutrient cycles affect rain forest ecology, and how ecologists investigate the complex interrelationships among flora and fauna. It covers tropical montane ecology, riverine ecosystems, savanna, dry forest--and more. Tropical Ecology begins with a historical overview followed by a sweeping discussion of biogeography and evolution, and then introduces students to the unique and complex structure of tropical rain forests. Other topics include the processes that influence everything from species richness to rates of photosynthesis: how global climate change may affect rain forest characteristics and function; how fragmentation of ecosystems affects species richness and ecological processes; human ecology in the tropics; biodiversity; and conservation of tropical ecosystems and species. {\textcopyright} 2011 by Princeton University Press. All Rights Reserved.},
-author = {Kricher, J.},
-isbn = {9780691115139 (ISBN)},
-journal = {Tropical Ecology},
-pages = {--},
-title = {{Tropical ecology}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84874205720{\&}partnerID=40{\&}md5=15307e962d33e447cb6a30bac68b5081},
-year = {2011}
-}
-@book{ConseilNationaldesArtsCulinaires1999,
-address = {Paris},
-author = {{Conseil National des Arts Culinaires}},
-booktitle = {L'inventaire du patrimoine culinaire de la France},
-editor = {Lebey, Claude},
-isbn = {2-226-10999-4},
-pages = {1--407},
-publisher = {Albin Michel},
-title = {{Guyane, produits du terroir et recettes traditionnelles}},
-year = {1999}
-}
-@article{Shipley2006,
-abstract = {Recent work has identified a worldwide "economic" spectrum of correlated leaf traits that affects global patterns of nutrient cycling and primary productivity and that is used to calibrate vegetation-climate models. The correlation patterns are displayed by species from the arctic to the tropics and are largely independent of growth form or phylogeny. This generality suggest that unidentified fundamental constraints control the return of photosynthates oil investments of nutrients and dry mass in leaves. Using novel graph theoretic methods and structural equation modeling, we show that the relationships among these variables can best be explained by assuming (1) a necessary trade-off between allocation to structural tissues versus liquid phase processes and (2) an evolutionary trade-off between leaf photosynthetic rates, construction costs, and leaf longevity.},
-author = {Shipley, Bill and Lechowicz, Martin J. and Wright, Ian J. and Reich, Peter B.},
-doi = {10.1890/05-1051},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shipley et al. - 2006 - Fundamental trade-offs generating the worldwide leaf economics spectrum.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {535--541},
-title = {{Fundamental trade-offs generating the worldwide leaf economics spectrum}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/05-1051/abstract},
-volume = {87},
-year = {2006}
-}
-@article{Sterck2006,
-abstract = {A dominant hypothesis explaining tree species coexistence in tropical forest is that trade-offs in characters allow species to adapt to different light environments, but tests for this hypothesis are scarce. This study is the first that uses a theoretical plant growth model to link leaf trade-offs to whole-plant performances and to differential performances across species in different light environments. Using data of 50 sympatric tree species from a Bolivian rain forest, we observed that specific leaf area and photosynthetic capacity codetermined interspecific height growth variation in a forest gap; that leaf survival rate determined the variation in plant survival rate under a closed canopy; that predicted height growth and plant survival rate matched field observations; and that fast-growing species had low survival rates for both field and predicted values. These results show how leaf trade-offs influence differential tree performance and tree species' coexistence in a heterogeneous light environment.},
-author = {Sterck, F. J. and Poorter, Lourens and Schieving, F.},
-doi = {10.1086/503056},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sterck, Poorter, Schieving - 2006 - Leaf traits determine the growth-survival trade-off across rain forest tree species.pdf:pdf},
-journal = {The American Naturalist},
-number = {5},
-pages = {758--765},
-title = {{Leaf traits determine the growth-survival trade-off across rain forest tree species}},
-url = {http://www.jstor.org/stable/10.1086/503056},
-volume = {167},
-year = {2006}
-}
-@article{Cronie2016,
-abstract = {We discuss and compare various approaches to the problem of bandwidth selection for kernel estimators of intensity functions of spatial point processes. We also propose a new method based on the Campbell formula applied to the reciprocal intensity function. The new method is fully non-parametric, does not require knowledge of the product densities, and is not restricted to a specific class of point process models.},
-archivePrefix = {arXiv},
-arxivId = {1611.10221},
-author = {Cronie, O. and van Lieshout, M. N. M.},
-eprint = {1611.10221},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cronie, van Lieshout - 2016 - Bandwidth selection for kernel estimators of the spatial intensity function.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Bandwidth selection for kernel estimators of the spatial intensity function}},
-url = {http://arxiv.org/abs/1611.10221},
-volume = {1611.10221},
-year = {2016}
-}
-@article{Kauppila2012,
-abstract = {Defining reference conditions for lakes situated in areas of human settlement and agriculture is rarely straightforward, and is especially difficult within easily eroding and nutrient rich watersheds. We used diatoms, cyanobaterial akinetes, remains of green algae and chironomid head capsules from sediment samples of Lake Kirmanj{\"{a}}rvi, Finland, to assess its deviation from the initial ecological status. These site-specific records of change were compared to current type-specific ecological status assessment. All paleolimnological data indicated deviation from natural conditions and mirrored the current, monitoring-based assessment of "moderate" ecological lake status. However, the sediment data showed that the lake should be re-typified as a naturally eutrophic lake. Sediment records as well as current monitoring data indicated temporary improvement in water quality in response to extensive fish manipulation. Our results suggest that paleolimnological records can be used to derive site-specific reference conditions and that extensive restoration efforts can result in gradual, observable improvements of water quality and ecological status. {\textcopyright} 2011 Elsevier GmbH.},
-author = {Kauppila, Tommi and Kanninen, Antti and Viitasalo, Matias and R{\"{a}}s{\"{a}}nen, Johanna and Meissner, Kristian and Mattila, Jukka},
-doi = {10.1016/j.limno.2011.07.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kauppila et al. - 2012 - Comparing long term sediment records to current biological quality element data - Implications for bioassessmen.pdf:pdf},
-journal = {Limnologica},
-number = {1},
-pages = {19--30},
-title = {{Comparing long term sediment records to current biological quality element data - Implications for bioassessment and management of a eutrophic lake}},
-url = {http://dx.doi.org/10.1016/j.limno.2011.07.001},
-volume = {42},
-year = {2012}
-}
-@article{Leclerc2015,
-abstract = {Key message Forest disturbance affects the within-population distribution of genetic diversity, but not its overall levels, in a tropical pioneer tree species. In particular, clumps of related saplings with impoverished diversity are found in canopy gaps but not under forest cover. Context Forest disturbances can have long-term consequences on the genetic structure of tree populations, because they can alter the demographic properties of the regeneration process and favour some subpopulations/genotypes, both by stochastic processes and by selection. Intermediate disturbances tend to favour species diversity, at least in highly diverse communities, but their effect on intra-specific diversity is unknown. Aims In this study, we have looked at the genetic consequences of forest disturbance in a stand of the long-lived Neotropical pioneer species, Jacaranda copaia. Methods The study site was experimentally logged in 1984, and the canopy gaps generated by the logging were mapped. Seedlings of J. copaia colonised the gaps, as expected, at a higher density than in the surrounding forest. In 2006, we exhaustively sampled all saplings and adult trees available in a 25-ha area. The samples were genotyped at nine microsatellite loci, and the distribution of genetic diversity was inspected by analyses of spatial autocorrelation, automated Bayesian assignment and comparisons of diversity between cohorts by bootstrap (RaBoT). Results Spatial autocorrelation was found to extend farther in post-disturbance saplings than in the undisturbed population (100 m and beyond versus less than 50 m), and divergent clumps (F ST = 0.05) of related genotypes were found; genetic diversity was found to be impoverished in each clump relative to the global population at about half of the loci. Conclusion Overall, our results suggest that forest disturbance has changed the patterns of distribution of genetic diversity, with potential consequences on long-term population viability.},
-author = {Leclerc, Thomas and Vimal, Ruppert and Troispoux, Val{\'{e}}rie and P{\'{e}}rigon, Sophie and Scotti, Ivan},
-doi = {10.1007/s13595-015-0462-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leclerc et al. - 2015 - Life after disturbance (I) changes in the spatial genetic structure of Jacaranda copaia (Aubl.) D. Don (Bignonia.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {5},
-pages = {509--516},
-title = {{Life after disturbance (I): changes in the spatial genetic structure of Jacaranda copaia (Aubl.) D. Don (Bignonianceae) after logging in an intensively studied plot in French Guiana}},
-url = {http://link.springer.com/10.1007/s13595-015-0462-0},
-volume = {72},
-year = {2015}
-}
-@article{Swenson2009,
-abstract = {Species diversity is promoted and maintained by ecological and evolutionary processes operating on species attributes through space and time. The degree to which variability in species function regulates distribution and promotes coexistence of species has been debated. Previous work has attempted to quantify the relative importance of species function by using phylogenetic relatedness as a proxy for functional similarity. The key assumption of this approach is that function is phylogenetically conserved. If this assumption is supported, then the phylogenetic dispersion in a community should mirror the functional dispersion. Here we quantify functional trait dispersion along several key axes of tree life-history variation and on multiple spatial scales in a Neotropical dry-forest community. We next compare these results to previously reported patterns of phylogenetic dispersion in this same forest. We find that, at small spatial scales, coexisting species are typically more functionally clustered than expected, but traits related to adult and regeneration niches are overdispersed. This outcome was repeated when the analyses were stratified by size class. Some of the trait dispersion results stand in contrast to the previously reported phylogenetic dispersion results. In order to address this inconsistency we examined the strength of phylogenetic signal in traits at different depths in the phylogeny. We argue that: (1) while phylogenetic relatedness may be a good general multivariate proxy for ecological similarity, it may have a reduced capacity to depict the functional mechanisms behind species coexistence when coexisting species simultaneously converge and diverge in function; and (2) the previously used metric of phylogenetic signal provided erroneous inferences about trait dispersion when married with patterns of phylogenetic dispersion. {\^{A}}{\textcopyright} 2009 by the Ecological Society of America.},
-annote = {Cited By (since 1996): 24
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: ECOLA
-doi: 10.1890/08-1025.1
-PubMed ID: 19739378
-Language of Original Document: English
-Correspondence Address: Swenson, N. G.; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, United States; email: nswenson@oeb.harvard.edu},
-author = {Swenson, Nathan G. and Enquist, Brian J.},
-doi = {10.1890/08-1025.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Swenson, Enquist - 2009 - Opposing assembly mechanisms in a Neotropical dry forest Implications for phylogenetic and functional communit.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {2161--2170},
-title = {{Opposing assembly mechanisms in a Neotropical dry forest: Implications for phylogenetic and functional community ecology}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-68149136776{\&}partnerID=40{\&}md5=b09a4fedf7c888b68b280f2bcea6e84c},
-volume = {90},
-year = {2009}
-}
-@article{Davies2016,
-abstract = {While there is good evidence linking animal introductions to impacts on native communities via disease emergence, our understanding ofhowsuch impacts occur is incomplete. Invasion ecologists have focused on the disease risks to native communities through ‘‘spillover'' of infectious agents introduced with nonindigenous hosts, while overlooking a potentially more common mechanism of impact, that of ‘‘parasite spillback.'' We hypothesize that parasite spillback could occur when a nonindigenous species is a competent host for a native parasite, with the presence of the additional host increasing disease impacts in native species. Despite its lack of formalization in all recent reviews of the role of parasites in species introductions, aspects of the invasion process actually favor parasite spillback over spillover.Wespecifically review the animal-parasite literature and show that native species (arthropods, parasitoids, protozoa, and helminths) account for 67{\%} of the parasite fauna of nonindigenous animals from a range of taxonomic groups. Weshow that nonindigenous species can be highly competent hosts for such parasites and provide evidence that infection by native parasites does spillback from nonindigenous species to native host species, with effects at both the host individual and population scale. We conclude by calling for greater recognition of parasite spillback as a potential threat to native species, discuss possible reasons for its neglect by invasion ecologists, and identify future research directions.},
-author = {Davies, T. Jonathan and Urban, Mark C. and Rayfield, Bronwyn and Cadotte, Marc W. and Peres-Neto, Pedro R.},
-doi = {10.1002/ecy.1507},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Davies et al. - 2016 - Deconstructing the relationships between phylogenetic diversity and ecology A case study on ecosystem functioning.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2212--2222},
-title = {{Deconstructing the relationships between phylogenetic diversity and ecology: A case study on ecosystem functioning}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/ecy.1507/abstract},
-volume = {97},
-year = {2016}
-}
-@article{Excoffier1992,
-abstract = {We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.},
-author = {Excoffier, Laurent and Smouse, Peter E. and Quattro, Joseph M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Excoffier, Smouse, Quattro - 1992 - Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes Application to Hu.pdf:pdf},
-journal = {Genetics},
-number = {2},
-pages = {479--491},
-title = {{Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data}},
-url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1205020/},
-volume = {131},
-year = {1992}
-}
-@article{Fawcett2012,
-abstract = {Most research in biology is empirical, yet empirical studies rely fundamentally on theoretical work for generating testable predictions and interpreting observations. Despite this interdependence, many empirical studies build largely on other empirical studies with little direct reference to relevant theory, suggesting a failure of communication that may hinder scientific progress. To investigate the extent of this problem, we analyzed how the use of mathematical equations affects the scientific impact of studies in ecology and evolution. The density of equations in an article has a significant negative impact on citation rates, with papers receiving 28{\%} fewer citations overall for each additional equation per page in the main text. Long, equation-dense papers tend to be more frequently cited by other theoretical papers, but this increase is outweighed by a sharp drop in citations from nontheoretical papers (35{\%} fewer citations for each additional equation per page in the main text). In contrast, equations presented in an accompanying appendix do not lessen a paper's impact. Our analysis suggests possible strategies for enhancing the presentation of mathematical models to facilitate progress in disciplines that rely on the tight integration of theoretical and empirical work.},
-author = {Fawcett, Tim W. and Higginson, Andrew D.},
-doi = {10.1073/pnas.1205259109},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fawcett, Higginson - 2012 - Heavy use of equations impedes communication among biologists.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {29},
-pages = {11735--9},
-title = {{Heavy use of equations impedes communication among biologists.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3406806{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {109},
-year = {2012}
-}
-@article{Diggle1997,
-abstract = {We describe a class of models for the investigation of possible raised risk of disease around putative sources of environmental pollution. An adaptation of the point process method suggested by Diggle and Rowlingson is presented, allowing the use of routinely available aggregated data and incorporating the more general distance-risk model suggested by Elliott and co-workers. An application to data on cancers of the stomach around municipal solid waste incinerators is presented.},
-author = {Diggle, Peter J. and Morris, Sara E. and Elliott, Paul and Shaddick, Gavin},
-doi = {10.1111/j.1467-985X.1997.00076.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle et al. - 1997 - Regression Modelling of Disease Risk in Relation to Point Sources.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {3},
-pages = {491--505},
-title = {{Regression Modelling of Disease Risk in Relation to Point Sources}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-985X.1997.00076.x/abstract},
-volume = {160},
-year = {1997}
-}
-@article{Fotheringham1991,
-abstract = {In this paper the examination of the modifiable areal unit problem is extended into multivariate statistical analysis. In an investigation of the parameter estimates from a multiple linear regression model and a multiple logit regression model, conclusions are drawn about the sensitivity of such estimates to variations in scale and zoning systems. The modifiable areal unit problem is shown to be essentially unpredictable in its intensity and effects in multivariate statistical analysis and is therefore a much greater problem than in univariate or bivariate analysis. The results of this analysis are rather depressing in that they provide strong evidence of the unreliability of any multivariate analysis undertaken with data from areal units. Given that such analyses can only be expected to increase with the imminent availability of new census data both in the United Kingdom and in the USA, and the current proliferation of GIS (geographical information system) technology which permits even more access to aggregated data, this paper serves as a topical warning.},
-author = {Fotheringham, A. S. and Wong, D. W. S.},
-doi = {10.1068/a231025},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fotheringham, Wong - 1991 - The modifiable areal unit problem in multivariate statistical analysis.pdf:pdf},
-journal = {Environment and Planning A},
-number = {7},
-pages = {1025--1044},
-title = {{The modifiable areal unit problem in multivariate statistical analysis}},
-url = {http://journals.sagepub.com/doi/abs/10.1068/a231025},
-volume = {23},
-year = {1991}
-}
-@article{Brulhart2001,
-abstract = {This paper analyses the geographical concentration of 32 manufacturing sectors over the 1972-1996 period, based on annual employment and export data for 13 European countries. Concentration has increased continuously over the sample period in employment terms, while remaining roughly unchanged in export terms. On average, increases in concentration were stronger prior to the launch of the Single Market than afterwards. The sectors most sensitive to the Single Market, however, showed an acceleration in concentration after 1986. There is also evidence that low-tech industries are the most strongly concentrated, and that centre-periphery gradients across countries are losing importance for industrial location in the EU.},
-author = {Br{\"{u}}lhart, Marius},
-doi = {10.1007/BF02707264},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Br{\"{u}}lhart - 2001 - Evolving Geographical Concentration of European Manufacturing Industries.pdf:pdf},
-journal = {Weltwirtschaftliches Archiv},
-number = {2},
-pages = {215--243},
-title = {{Evolving Geographical Concentration of European Manufacturing Industries}},
-url = {https://link.springer.com/article/10.1007/BF02707264},
-volume = {137},
-year = {2001}
-}
-@article{Kenkel1989,
-author = {Kenkel, N. C. and Hoskins, J. A. and Hoskins, W. D.},
-doi = {10.2307/1938433},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kenkel, Hoskins, Hoskins - 1989 - Edge Effects in the Use of Area Polygons to Study Competition.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {272--274},
-title = {{Edge Effects in the Use of Area Polygons to Study Competition}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1938433/full},
-volume = {70},
-year = {1989}
-}
-@article{Hoorn2010,
-abstract = {The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.},
-author = {Hoorn, C. and Wesselingh, F. P. and ter Steege, Hans and Bermudez, M. A. and Mora, A. and Sevink, J. and Sanmart{\'{i}}n, I. and Sanchez-Meseguer, A. and Anderson, C. L. and Figueiredo, J. P. and Jaramillo, C. and Riff, D. and Negri, F. R. and Hooghiemstra, H. and Lundberg, J. and Stadler, T. and S{\"{a}}rkinen, T. and Antonelli, A.},
-doi = {10.1126/science.1194585},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hoorn et al. - 2010 - Amazonia Through Time Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity.pdf:pdf},
-journal = {Science},
-number = {6006},
-pages = {927--931},
-title = {{Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity}},
-url = {http://www.sciencemag.org/content/330/6006/927.abstract},
-volume = {330},
-year = {2010}
-}
-@article{Grilli2012,
-abstract = {There has been a considerable effort to understand and quantify the spatial distribution of species across different ecosystems. Relative species abundance (RSA), beta diversity and species–area relationship (SAR) are among the most used macroecological measures to characterize plants communities in forests. In this paper we introduce a simple phenomenological model based on Poisson cluster processes which allows us to exactly link RSA and beta diversity to SAR. The framework is spatially explicit and accounts for the spatial aggregation of conspecific individuals. Under the simplifying assumption of neutral theory, we derive an analytical expression for the SAR which reproduces tri-phasic behavior as sample area increases from local to continental scales, explaining how the tri-phasic behavior can be understood in terms of simple geometric arguments. We also find an expression for the endemic area relationship (EAR) and for the scaling of the RSA.},
-author = {Grilli, Jacopo and Azaele, Sandro and Banavar, Jayanth R. and Maritan, Amos},
-doi = {10.1016/j.jtbi.2012.07.030},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grilli et al. - 2012 - Spatial aggregation and the species–area relationship across scales.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {0},
-pages = {87--97},
-title = {{Spatial aggregation and the species–area relationship across scales}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519312003839},
-volume = {313},
-year = {2012}
-}
-@article{Ryman2009,
-annote = {ISI Document Delivery No.: 441MW
-Times Cited: 6
-Cited Reference Count: 19
-Ryman, Nils Leimar, Olof
-WILEY-BLACKWELL PUBLISHING, INC},
-author = {Ryman, Nils and Leimar, Olof},
-doi = {10.1111/j.1365-294X.2009.04187.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ryman, Leimar - 2009 - G(ST) is still a useful measure of genetic differentiation - a comment on Jost's D.pdf:pdf},
-journal = {Molecular Ecology},
-number = {10},
-pages = {2084--2087},
-title = {{G(ST) is still a useful measure of genetic differentiation - a comment on Jost's D}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2009.04187.x/abstract},
-volume = {18},
-year = {2009}
-}
-@article{Abe2001,
-abstract = {Based on the form invariance of the structures given by Khinchin's axiomatic foundations of information theory and the pseudoadditivity of the Tsallis entropy indexed by q, the concept of conditional entropy is generalized to the case of nonadditive (nonextensive) composite systems. The proposed nonadditive conditional entropy is classically nonnegative but can be negative in the quantum context, indicating its utility for characterizing quantum entanglement. A criterion deduced from it for separability of density matrices for validity of local realism is examined in detail by employing a bipartite spin-1=2 system. It is found that the strongest criterion is obtained in the limit q→∞.},
-author = {Abe, Sumiyoshi and Rajagopal, A. K.},
-doi = {10.1016/S0378-4371(00)00476-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Abe, Rajagopal - 2001 - Nonadditive conditional entropy and its significance for local realism.pdf:pdf},
-journal = {Physica A},
-number = {1-2},
-pages = {157--164},
-title = {{Nonadditive conditional entropy and its significance for local realism}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378437100004763},
-volume = {289},
-year = {2001}
-}
-@book{Kimura1983,
-abstract = {Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. He first proposed the theory in 1968 to explain the unexpectedly high rate of evolutionary change and very large amount of intraspecific variability at the molecular level that had been uncovered by new techniques in molecular biology. The theory - which asserts that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants - has caused controversy ever since. This book is the first comprehensive treatment of this subject and the author synthesises a wealth of material - ranging from a historical perspective, through recent molecular discoveries, to sophisticated mathematical arguments - all presented in a most lucid manner.},
-author = {Kimura, Motoo},
-booktitle = {The neutral theory of molecular evolution},
-isbn = {0521317932},
-pages = {367},
-title = {{The Neutral Theory of Molecular Evolution}},
-url = {http://books.google.co.il/books?id=olIoSumPevYC{\&}lpg=PP1{\&}dq=the neutral theory of molecular evolution{\%}5Cnhttps://books.google.com/books?hl=en{\&}lr={\&}id=olIoSumPevYC{\&}pgis=1},
-year = {1983}
-}
-@book{Swenson2014,
-abstract = {Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.},
-author = {Swenson, Nathan G.},
-booktitle = {Use R!},
-doi = {10.1007/978-1-4614-9542-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Swenson - 2014 - Functional and Phylogenetic Ecology in R.pdf:pdf},
-isbn = {9781461495420},
-pages = {217},
-publisher = {Springer},
-title = {{Functional and Phylogenetic Ecology in R}},
-year = {2014}
-}
-@article{Moles2005,
-abstract = {We used correlated divergence analysis to determine which factors have been most closely associated with changes in seed mass during seed plant evolution. We found that divergences in seed mass have been more consistently associated with divergences in growth form than with divergences in any other variable. This finding is consistent with the strong relationship between seed mass and growth form across present-day species and with the available data from the paleobotanical literature. Divergences in seed mass have also been associated with divergences in latitude, net primary productivity, temperature, precipitation, and leaf area index. However, these environmental variables had much less explanatory power than did plant traits such as seed dispersal syndrome and plant growth form.},
-author = {Moles, Angela T. and Ackerly, David D. and Webb, Campbell O. and Tweddle, J. C. and Dickie, J. B. and Pitman, A. J. and Westoby, Mark},
-doi = {10.1073?pnas.0501473102},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moles et al. - 2005 - Factors that shape seed mass evolution.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {30},
-pages = {10540--10544},
-title = {{Factors that shape seed mass evolution}},
-volume = {102},
-year = {2005}
-}
-@incollection{Mayden1997,
-abstract = {At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous to classifications of supraspecific taxa, our forging inappropriate and ambiguous information relating to theoretical and operational discussions of species ultimately results in a trade-off between convenience, accuracy, precision, and the successful recovery of natural biological diversity. Hence, none of these expectations or intentions of species or classifications is attainable through composite, and possibly discordant, concepts of biological diversity or its descent. Reviowing and evaluating the concepts of species for their theoretical and operational qualities illustrates that a monistic, primary conept of species, applicable to the various entiies believed to be species, is essential. this evaluation reveals only one theoretical concept as appropriate for species, the Evolutionary Species Concept. This conceptualiztion functions as a primary concept and is essential in structuring our ideas and perceptions of real species in the natural world. The remaining concepts are secondary, forming a hierarchy of definitional guidelines subordinate to the primary concept, and are essential to the study of species in practice. Secondary concepts....},
-address = {London},
-author = {Mayden, Richard L.},
-booktitle = {Species. The units of biodiversity.},
-chapter = {19},
-editor = {Claridge, M. F. and Dawah, H. A. and Wilson, M. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mayden - 1997 - A hierarchy of species concepts the denouement in the saga of the species problem.pdf:pdf},
-issn = {03092593},
-pages = {381--424},
-pmid = {3720},
-publisher = {Chapman and Hall},
-title = {{A hierarchy of species concepts: the denouement in the saga of the species problem}},
-year = {1997}
-}
-@article{Pearson1901,
-author = {Pearson, Karl},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pearson - 1901 - On lines and planes of closest fit to systems of points in space.pdf:pdf},
-journal = {Philosophical Magazine},
-pages = {559--572},
-title = {{On lines and planes of closest fit to systems of points in space}},
-url = {http://www.tandfonline.com/doi/pdf/10.1080/14786440109462720},
-volume = {2},
-year = {1901}
-}
-@book{Florence1939,
-address = {London},
-annote = {D{\'{e}}finition du quotient de localisation.},
-author = {Florence, P. S.},
-publisher = {Political and Economic Planning},
-title = {{Report of the location of industry}},
-year = {1939}
-}
-@article{Chen2015,
-abstract = {Leprieur and Oikonomou (2014) criticized that a replacement index $\beta$−3, a partitioned component of Jaccard index $\beta$jac, was not richness independent and should not be used in biogeographic and ecological studies. However, Leprieur and Oikonomou failed to recognize the difference between richness and richness difference. Independence of total species richness is not equal to independence of richness difference. Theoretically and ideally, it is true that $\beta$−3 (and $\beta$jac as well) is not independent of richness difference while Simpson index ($\beta$sim) is fully independent of richness difference. However, all these indices actually are independent of total species richness. At last, it is worth mentioning that the ideal independence studied here is easily violated in computational simulation and real-world settings.},
-author = {Chen, Youhua},
-doi = {10.1016/j.ecoinf.2015.10.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chen - 2015 - Independence of total species richness and richness difference are not the same thing.pdf:pdf},
-journal = {Ecological Informatics},
-pages = {119--123},
-title = {{Independence of total species richness and richness difference are not the same thing}},
-url = {http://www.sciencedirect.com/science/article/pii/S1574954115001612},
-volume = {30},
-year = {2015}
-}
-@phdthesis{Puech2003,
-address = {Paris},
-author = {Puech, Florence},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Puech - 2003 - Concentration g{\'{e}}ographique des activit{\'{e}}s industrielles Mesures et enjeux.pdf:pdf},
-publisher = {Universit{\'{e}} de Paris I, Panth{\'{e}}on - Sorbonne},
-title = {{Concentration g{\'{e}}ographique des activit{\'{e}}s industrielles : Mesures et enjeux}},
-volume = {PhD},
-year = {2003}
-}
-@article{Schmera2013,
-abstract = {Diversity partitioning has been generally used to estimate the contribution of different levels of sampling hierarchy to landscape diversity. However, beta diversity values derived by partitioning strongly depend on focus and sample size and the partitioning is inadequate to express the contribution of landscape elements to community variation. Pairwise dissimilarities are also frequently used to express community turnover, but related approaches capture only limited aspects of it, especially for hierarchical sampling designs. To avoid these shortcomings, we suggest a procedure which quantifies the role of different levels of sampling hierarchy (relative beta diversity) and the share of landscape elements in the corresponding relative beta diversity (contribution value). Our novel method uses pairwise dissimilarities and is based on partitioning a dissimilarity matrix of sampling units. It is suitable to testing various null hypotheses via permutation techniques as demonstrated by artificial and actual data. The method is a valuable tool in ecology because it complements existing approaches while providing a unique way to understand community diversity in space.},
-author = {Schmera, D{\'{e}}nes and Podani, J{\'{a}}nos},
-doi = {http://dx.doi.org/10.1016/j.ecolind.2012.10.029},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schmera, Podani - 2013 - Components of beta diversity in hierarchical sampling designs A new approach.pdf:pdf},
-journal = {Ecological Indicators},
-number = {0},
-pages = {126--136},
-title = {{Components of beta diversity in hierarchical sampling designs: A new approach}},
-url = {http://www.sciencedirect.com/science/article/pii/S1470160X12003809},
-volume = {26},
-year = {2013}
-}
-@article{Ricotta2001,
-abstract = {Several evenness measures have been proposed for quantifying the distribution of abundance among community species, but none seems to be generally preferred. Since these measures have the common objective of summarizing community structure, they may be expected to be incorrelated. In this paper, seven standard measures of evenness were calculated for 65 sample plots of ruderal vegetation within the archaeological sites of Paestum and Venosa (southern Italy). Principal component analysis was used to identify the primary aspects of community structure being characterized by these seven indices. The first two principal components explained 96{\%} of total varrance A comparison of the first two principal components with the analyzed measures of evenness provides insight into what aspects of community structure they are expressing. While the first principal component is most sensitive to the relative abundances of rare species, the second principal component is clearly associated to changes in the abundance of the dominant community species.},
-annote = {Cited By (since 1996): 7
-Export Date: 28 December 2011
-Source: Scopus
-CODEN: CEOCA
-doi: 10.1556/ComEc.2.2001.1.6
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, Rome 00185, Italy; email: carlo.ricotta@uniromal.it},
-author = {Ricotta, Carlo and {De Zuliani}, E. and Pacini, A. and Avena, Giancarlo C.},
-doi = {10.1556/ComEc.2.2001.1.6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2001 - On the mutual relatedness of evenness measures.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {51--56},
-title = {{On the mutual relatedness of evenness measures}},
-url = {http://akademiai.com/doi/abs/10.1556/ComEc.2.2001.1.6},
-volume = {2},
-year = {2001}
-}
-@inproceedings{Renyi1961,
-address = {Berkeley, USA},
-author = {R{\'{e}}nyi, Alfr{\'{e}}d},
-booktitle = {4th Berkeley Symposium on Mathematical Statistics and Probability},
-editor = {Neyman, Jerzy},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/R{\'{e}}nyi - 1961 - On Measures of Entropy and Information.pdf:pdf},
-pages = {547--561},
-publisher = {University of California Press},
-title = {{On Measures of Entropy and Information}},
-volume = {1},
-year = {1961}
-}
-@article{Tsallis1988,
-abstract = {With the use of a quantity normally scaled in multifractals, a generalized form is postulated for entropy, namelySq =k [1 – ?i=1W piq]/(q-1), whereq?R characterizes the generalization andpi are the probabilities associated withW (microscopic) configurations (W?N). The main properties associated with this entropy are established, particularly those corresponding to the microcanonical and canonical ensembles. The Boltzmann-Gibbs statistics is recovered as theq?1 limit.},
-annote = {10.1007/BF01016429},
-author = {Tsallis, Constantino},
-doi = {10.1007/BF01016429},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tsallis - 1988 - Possible generalization of Boltzmann-Gibbs statistics.pdf:pdf},
-journal = {Journal of Statistical Physics},
-number = {1},
-pages = {479--487},
-title = {{Possible generalization of Boltzmann-Gibbs statistics}},
-url = {http://dx.doi.org/10.1007/BF01016429},
-volume = {52},
-year = {1988}
-}
-@book{Wilson1984a,
-address = {Cambridge, Massachusetts, and London, England},
-author = {Wilson, Edward O.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilson - 1984 - Biophilia.pdf:pdf},
-isbn = {0674074416},
-publisher = {Harvard University Press},
-title = {{Biophilia}},
-year = {1984}
-}
-@article{Veresoglou2014,
-abstract = {An increasing number of ecological studies compare the diversity of microbial taxa along environmental gradients or between imposed treatments. Estimates are often based on analysis-of-variance of taxon-richness inferred from pyrosequencing data.Weconducted a reanalysis of three 454-pyrosequencing studies on arbuscular-mycorrhizal-fungal diversity to evaluate the suitability of using the Leinster and Cobbold diversity-indices (LCdis) to assess diversity. We expected that the potential of LCdis to consider phylogenic relation- ships could resolve problems arising from ambiguous species-delineation in microbial- systems. Our reanalysis showed that comparisons between studies differing consid- erably in sequencing depth may be risky. Moreover, we show that LCdis not only reproduce the results of analyses of variance but can also resolve issues connected to variation in sequence read number, while additionally representing a less conservative metric of diversity than analysis-of-variance of taxa-richness. Based on these results we advocate the use of inclusive diversity indices in ecological studies targeting microbial communities.},
-author = {Veresoglou, Stavros D. and Powell, Jeff R. and Davison, John and Lekberg, Ylva and Rillig, Matthias C.},
-doi = {10.1016/j.funeco.2014.03.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veresoglou et al. - 2014 - The Leinster and Cobbold indices improve inferences about microbial diversity.pdf:pdf},
-journal = {Fungal Ecology},
-pages = {1--7},
-title = {{The Leinster and Cobbold indices improve inferences about microbial diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1754504814000440},
-volume = {11},
-year = {2014}
-}
-@article{Soliveres2016,
-abstract = {Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend1, 2. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa3, 4 and that the functional effects of any trophic group may depend on the abundance and diversity of others5, 6. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for ‘regulating' and ‘cultural' services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results7, 8 to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.},
-author = {Soliveres, Santiago and van der Plas, Fons and Manning, Peter and Prati, Daniel and Gossner, Martin M. and Renner, Swen C. and Alt, Fabian and Arndt, Hartmut and Baumgartner, Vanessa and Binkenstein, Julia and Birkhofer, Klaus and Blaser, Stefan and Bl{\"{u}}thgen, Nico and Boch, Steffen and B{\"{o}}hm, Stefan and B{\"{o}}rschig, Carmen and Buscot, Francois and Diek{\"{o}}tter, Tim and Heinze, Johannes and H{\"{o}}lzel, Norbert and Jung, Kirsten and Klaus, Valentin H. and Kleinebecker, Till and Klemmer, Sandra and Krauss, Jochen and Lange, Markus and Morris, E. Kathryn and M{\"{u}}ller, J{\"{o}}rg and Oelmann, Yvonne and Overmann, J{\"{o}}rg and Pa{\v{s}}ali{\'{c}}, Esther and Rillig, Matthias C. and Schaefer, H. Martin and Schloter, Michael and Schmitt, Barbara and Sch{\"{o}}ning, Ingo and Schrumpf, Marion and Sikorski, Johannes and Socher, Stephanie A. and Solly, Emily F. and Sonnemann, Ilja and Sorkau, Elisabeth and Steckel, Juliane and Steffan-Dewenter, Ingolf and Stempfhuber, Barbara and Tschapka, Marco and T{\"{u}}rke, Manfred and Venter, Paul C. and Weiner, Christiane N. and Weisser, Wolfgang W. and Werner, Michael and Westphal, Catrin and Wilcke, Wolfgang and Wolters, Volkmar and Wubet, Tesfaye and Wurst, Susanne and Fischer, Markus and Allan, Eric},
-doi = {10.1038/nature19092},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Soliveres et al. - 2016 - Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality.pdf:pdf},
-journal = {Nature},
-number = {7617},
-pages = {456--459},
-publisher = {Nature Publishing Group},
-title = {{Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality}},
-url = {http://dx.doi.org/10.1038/nature19092},
-volume = {536},
-year = {2016}
-}
-@techreport{Devereux1999,
-abstract = {There has much recent academic and policy interest in the issue of spatial clustering of economic activity, with most attention paid to the geographic concentration of high-tech industries. This paper describes patterns of geographic and industrial concentration in UK production industries at the 4-digit industry level. Several measures are used, including a new simple and intuitive measure of agglomeration. Conditioning on industrial concentration, many of the most geographically concentrated industries are not high-tech industries. We find that the most agglomerated industries are relatively low-tech and that they have lower entry and exit rates and higher survival rates as well as lower job creation and job destruction rates. Within industries we find that the most concentrated region has, on average, lower entry and exit rates but higher job creation rates and lower job destruction rates.},
-author = {Devereux, Michael P. and Griffith, Rachel and Simpson, Helen},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Devereux, Griffith, Simpson - 1999 - The Geographic Distribution of Production Activity in the UK.pdf:pdf},
-publisher = {The Institute for Financial Studies},
-title = {{The Geographic Distribution of Production Activity in the UK}},
-url = {http://www.ifs.org.uk/workingpapers/wp2699.pdf},
-year = {1999}
-}
-@techreport{Paradis2002,
-author = {Paradis, Emmanuel},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Paradis - 2002 - R pour les d{\'{e}}butants.pdf:pdf},
-publisher = {Universit{\'{e}} Montpellier 2},
-title = {{R pour les d{\'{e}}butants}},
-url = {https://cran.r-project.org/doc/contrib/Paradis-rdebuts{\_}fr.pdf},
-year = {2002}
-}
-@article{Scheiner2016,
-abstract = {One aspect of biodiversity, functional diversity, reflects the functional role of species within a community as measured by species characteristics. We present a new metric, functional trait dispersion, based on the concept of species distinctiveness measured as the distance among species in the multidimensional space defined by trait values. This metric can be decomposed into components of species richness, functional evenness and mean dispersion, and into parts that measure diversity within and among subgroups. Using an appropriate distance measure, mean dispersion (M′) is calculated as the average distance among all possible pairs of species. Functional evenness [qE(T)] is derived from Hill diversity based on the proportional distances between pairs of species and species richness (S). Functional trait dispersion [qD(TM)] is then computed as 1 + (S−1) × qE(T) × M′. It has a range of [1,S] and measures the effective number of functionally distinct species for a given level of species dispersion. Using constructed data, we demonstrate that qD(TM) captures appropriate ecological properties such that a community with greater species richness, greater dispersal in trait space or greater mean dispersion has greater functional diversity. Functional trait dispersion can also provide measures of within-community dispersion and the effective number of functionally distinctive compartments (groups of communities with similar functional structure). Using empirical data of bats along an elevational gradient in Peru, we demonstrate that functional trait dispersion and its components provide insights about gradients of biodiversity. Functional trait dispersion comports to reasonable criteria for a metric of functional diversity and can be decomposed in a variety of ways that facilitate understanding of patterns of variation. Other metrics of functional diversity neither integrate all three diversity components, nor can many be decomposed into variation within and among subgroups. Because functional trait dispersion measures properties of distance and the effective number of functionally distinct species, it can be used in conjunction with other biodiversity metrics that are based on species identity, abundance or phylogenetic relatedness to inform management and the preservation of biodiversity.},
-author = {Scheiner, Samuel M. and Kosman, Evsey and Presley, Steven J. and Willig, Michael R.},
-doi = {10.1111/2041-210X.12696},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scheiner et al. - 2017 - Decomposing functional diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {7},
-pages = {809--820},
-title = {{Decomposing functional diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12696/abstract},
-volume = {8},
-year = {2017}
-}
-@article{Renkonen1938,
-author = {Renkonen, Olavi},
-journal = {Annales botanici Societatis Zoologic{\ae} Botanic{\ae} Fennic{\ae} Vanamo},
-pages = {1--231},
-title = {{Statisch-{\"{o}}kologische Untersuchungen {\"{u}}ber die terrestrische K{\"{a}}ferwelt der finnischen Bruchmoore}},
-volume = {6},
-year = {1938}
-}
-@article{Arbia2001a,
-abstract = {Economists have recently devoted an increasing attention to the issue of spatial concentration of economic activities. However, surprisingly enough, most of the empirical work is still based on the computation of very basic statistical measures in which the geographical characteristics of data play no role. By making use of a series of empirical examples we show that spatial concentration consists of two different features that are rarely kept as separate in the statistical analysis: an a-spatial concept of variability which is invariant to permutations, and the concept of polarization that refers to the geographical position of observations.},
-author = {Arbia, Giuseppe},
-doi = {10.1007/PL00011480},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia - 2001 - The Role of Spatial Effects in the Empirical Analysis of Regional Concentration.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {3},
-pages = {271--281},
-title = {{The Role of Spatial Effects in the Empirical Analysis of Regional Concentration}},
-url = {http://link.springer.com/article/10.1007/PL00011480},
-volume = {3},
-year = {2001}
-}
-@article{Jost2009,
-author = {Jost, Lou},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2009 - Mismeasuring biological diversity Response to Hoffmann and Hoffmann (2008).pdf:pdf},
-journal = {Ecological Economics},
-pages = {925--928},
-title = {{Mismeasuring biological diversity: Response to Hoffmann and Hoffmann (2008)}},
-volume = {68},
-year = {2009}
-}
-@phdthesis{Jabot2009,
-address = {Toulouse},
-author = {Jabot, Franck},
-booktitle = {Ecole doctorale SEVAB},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jabot - 2009 - Marches al{\'{e}}atoires en for{\^{e}}t tropicale, Contribution {\`{a}} la th{\'{e}}orie de la biodiversit{\'{e}}.pdf:pdf},
-publisher = {Universit{\'{e}} Toulouse III – Paul Sabatier},
-title = {{Marches al{\'{e}}atoires en for{\^{e}}t tropicale, Contribution {\`{a}} la th{\'{e}}orie de la biodiversit{\'{e}}}},
-year = {2009}
-}
-@article{Eren2012,
-abstract = {Background: Estimating assemblage species or class richness from samples remains a challenging, but essential, goal. Though a variety of statistical tools for estimating species or class richness have been developed, they are all singly-bounded: assuming only a lower bound of species or classes. Nevertheless there are numerous situations, particularly in the cultural realm, where the maximum number of classes is fixed. For this reason, a new method is needed to estimate richness when both upper and lower bounds are known. Methodology/Principal Findings: Here, we introduce a new method for estimating class richness: doubly-bounded confidence intervals (both lower and upper bounds are known). We specifically illustrate our new method using the Chao1 estimator, rarefaction, and extrapolation, although any estimator of asymptotic richness can be used in our method. Using a case study of Clovis stone tools from the North American Lower Great Lakes region, we demonstrate that singly-bounded richness estimators can yield confidence intervals with upper bound estimates larger than the possible maximum number of classes, while our new method provides estimates that make empirical sense. Conclusions/Significance: Application of the new method for constructing doubly-bound richness estimates of Clovis stone tools permitted conclusions to be drawn that were not otherwise possible with singly-bounded richness estimates, namely, that Lower Great Lakes Clovis Paleoindians utilized a settlement pattern that was probably more logistical in nature than residential. However, our new method is not limited to archaeological applications. It can be applied to any set of data for which there is a fixed maximum number of classes, whether that be site occupancy models, commercial products (e. g. athletic shoes), or census information (e. g. nationality, religion, age, race).},
-annote = {ISI Document Delivery No.: 959WT
-Times Cited: 0
-Cited Reference Count: 55
-Eren, Metin I. Chao, Anne Hwang, Wen-Han Colwell, Robert K.
-Public library science
-San francisco},
-author = {Eren, Metin I. and Chao, Anne and Hwang, Wen-Han and Colwell, Robert K.},
-doi = {10.1371/journal.pone.0034179},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eren et al. - 2012 - Estimating the Richness of a Population When the Maximum Number of Classes Is Fixed A Nonparametric Solution to an.pdf:pdf},
-journal = {Plos One},
-number = {5},
-title = {{Estimating the Richness of a Population When the Maximum Number of Classes Is Fixed: A Nonparametric Solution to an Archaeological Problem}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034179},
-volume = {7},
-year = {2012}
-}
-@article{Albert2002,
-abstract = {Spatial point processes form a set of statistical tools capable of modelling many environmental processes. They can deal with spatial interactions and dependencies between individuals which is an essential framework in environmental modelling. In this context, we focus on inhibitory pairwise interaction point processes that can be obtained as the limit of a suitable sequence of auto-Poisson lattice schemes. We review the limit theorems concerned, present a computer software (SPPA) and analyze the results of a Monte Carlo simulation study based on a particular pairwise interaction model. (C) 2002 Elsevier Science Ltd. All rights reserved.},
-author = {Albert, J. M. and Mateu, Jorge and Pernias, J. C.},
-doi = {10.1016/S1364-8152(01)00041-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Albert, Mateu, Pernias - 2002 - Modelling of spatial point processes derived from a sequence of auto-Poisson lattice schemes.pdf:pdf},
-journal = {Environmental Modelling {\&} Software},
-number = {2},
-pages = {107--125},
-title = {{Modelling of spatial point processes derived from a sequence of auto-Poisson lattice schemes}},
-volume = {17},
-year = {2002}
-}
-@article{Tilman1994,
-abstract = {All organisms, especially terrestrial plants and other sessile species, interact mainly with their neighbors, but neighborhoods can differ in composition because of dispersal and mortality. There is increasingly strong evidence that the spatial structure created by these forces profoundly influences the dynamics, composition, and biodiversity of communities. Nonspatial models predict that no more consumer species can coexist at equilibrium than there are limiting resources. In contrast, a similar model that includes neighborhood competition and random dispersal among sites predicts stable coexistence of a potentially unlimited number of species on a single resource. Coexistence occurs because species with sufficiently high dispersal rates persist in sites not occupied by superior competitors. Coexistence requires limiting similarity and two—way or three—way interspecific trade—offs among competitive ability, colonization ability, and longevity. This spatial competition hypothesis seems to explain the coexistence of the numerous plant species that compete for a single limiting resource in the grasslands of Cedar Creek Natural History Area. It provides a testable, alternative explanation for other high diversity communities, such as tropical forests. The model can be tested (1) by determining if coexisting species have the requisite trade—offs in colonization, competition, and longevity, (2) by addition of propagules of propagules to determine if local species abundances are limited by dispersal, and (3) by comparisons of the effects on biodiversity of high rates of propagule addition for species that differ in competitive ability.},
-author = {Tilman, David},
-doi = {10.2307/1939377},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tilman - 1994 - Competition and biodiversity in spatially structured habitats.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {2--16},
-title = {{Competition and biodiversity in spatially structured habitats}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1939377/full},
-volume = {75},
-year = {1994}
-}
-@article{Kosman2005,
-abstract = {Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)-vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well-founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals' phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.},
-author = {Kosman, Evsey and Leonard, Kurt J},
-doi = {10.1111/j.1365-294X.2005.02416.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosman, Leonard - 2005 - Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haplo.pdf:pdf},
-journal = {Molecular ecology},
-number = {2},
-pages = {415--24},
-title = {{Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/15660934},
-volume = {14},
-year = {2005}
-}
-@article{Pueyo2007,
-abstract = {Why does the neutral theory, which is based on unrealistic assumptions, predict diversity patterns so accurately? Answering questions like this requires a radical change in the way we tackle them. The large number of degrees of freedom of ecosystems pose a fundamental obstacle to mechanistic modelling. However, there are tools of statistical physics, such as the maximum entropy formalism (MaxEnt), that allow transcending particular models to simultaneously work with immense families of models with different rules and parameters, sharing only well-established features. We applied MaxEnt allowing species to be ecologically idiosyncratic, instead of constraining them to be equivalent as the neutral theory does. The answer we found is that neutral models are just a subset of the majority of plausible models that lead to the same patterns. Small variations in these patterns naturally lead to the main classical species abundance distributions, which are thus unified in a single framework.},
-author = {Pueyo, Salvador and He, Fangliang and Zillio, Tommaso},
-doi = {10.1111/j.1461-0248.2007.01096.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pueyo, He, Zillio - 2007 - The maximum entropy formalism and the idiosyncratic theory of biodiversity.pdf:pdf},
-journal = {Ecology letters},
-number = {11},
-pages = {1017--28},
-title = {{The maximum entropy formalism and the idiosyncratic theory of biodiversity}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2121135{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {10},
-year = {2007}
-}
-@article{Brown2011,
-abstract = {1. Attempts to infer underlying ecological process from observed patterns in ecology have been widespread, but have generally relied on first-order (non-spatial) community characteristics such as the species abundance distribution (SAD). This measure has become an important test of several theories of species coexistence, but has proved unsuccessful in distinguishing between them. 2. Spatially explicit data are increasingly available for a range of ecological communities, and analysis methods for these data are well developed. However, relatively little work has investigated the potential of these data for similar inference about mechanisms of coexistence. 3. In this study, we systematically investigate the spatial and non-spatial signals of simulated ecological processes. We include neutral, niche, lottery, Janzen-Connell and heteromyopia models, deriving and comparing first-and second-order measures for the patterns they generate. 4. We find that the SAD is unable to distinguish reliably between underlying models, with random variation in its shape concealing any systematic differences. 5. A new second-order summary measure of spatial structure derived in this paper, in contrast, proves highly sensitive to the type of ecological interaction being modelled, and is robust to random variation. 6. Synthesis. A simple summary measure of the spatial structure of plant communities is presented and found to be a more powerful indicator of underlying process in simulated data than a widely used first-order measure, the SAD. The potential for answering important ecological questions using spatial statistics, particularly concerning mechanisms of coexistence in diverse communities, appears to be great.},
-annote = {ISI Document Delivery No.: 840FR
-Times Cited: 0
-Cited Reference Count: 69
-Brown, Calum Law, Richard Illian, Janine B. Burslem, David F. R. P.
-Microsoft PhD Scholarship
-This work required a great deal of computing time for simulations, the majority of which were run on the RINH/BioSS Beowulf cluster at the University of Aberdeen Rowett Institute of Nutrition and Health (http://bioinformatics.rri.sari.ac.uk). We thank Tony Travis, Kevin Hammond, Vladimir Janjic, Herbert Fruchtl, Greg Michaelson and Evan Brown for their assistance in running all simulations. We are also grateful for useful discussions with Angelika Studeny and Glenna Evans, and to two anonymous referees for their insightful and helpful comments. C.B. is funded by a Microsoft PhD Scholarship.
-Wiley-blackwell
-Malden},
-author = {Brown, Calum and Law, Richard and Illian, Janine B. and Burslem, David F. R. P.},
-doi = {10.1111/j.1365-2745.2011.01877.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brown et al. - 2011 - Linking ecological processes with spatial and non-spatial patterns in plant communities.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {1402--1414},
-title = {{Linking ecological processes with spatial and non-spatial patterns in plant communities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2011.01877.x/abstract},
-volume = {99},
-year = {2011}
-}
-@article{Mora2004,
-abstract = {This paper analyzes the evolution of agricultural product specialisation at the farm and county levels in Spain from 1979 to 1997. This period covers all the stages of the gradual implementation of the Common Agricultural Policy and the integration of the Spanish agriculture into the European Market. A multiple product version of Theil and Finizza's indices of segregation is used to decompose farm product specialisation into county specialisation with respect to the national level and farm specialisation within counties. Using a probit specification, we test whether changes in specialisation are driven by comparative advantage at regional level or have been policy induced. Our results confirm the existence of increasing county specialisation and highlight the fact that counties which were initially more specialised in export-oriented products have shown the largest increase in specialisation.},
-author = {Mora, Ricardo and {San Juan}, Carlos},
-doi = {10.1016/S0166-0462(03)00042-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mora, San Juan - 2004 - Geographical specialisation in Spanish agriculture before and after integration in the European Union.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {3},
-pages = {309-- 320},
-title = {{Geographical specialisation in Spanish agriculture before and after integration in the European Union}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046203000425},
-volume = {34},
-year = {2004}
-}
-@article{May1990,
-abstract = {This paper begins with a survey of the patterns in discovering and recording species of animals and plants, from Linnaeus' time to the present. It then outlines various approaches to estimating what the total number of species on Earth might be: these approaches include extrapolation of past trends; direct assessments based on the overall fraction previously recorded among newly studied groups of tropical insects; indirect assessment derived from recent studies of arthropods in the canopies of tropical trees (giving special attention to the question of what fraction of the species found on a given host-tree are likely to be `effectively specialized' on it); and estimates inferred from theoretical and empirical patterns in speciessizes relations or in food web structure. I conclude with some remarks on the broader implications of our ignorance about how many species there are.},
-author = {May, Robert M. and Beverton, R. J. H.},
-doi = {10.1098/rstb.1990.0200},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May, Beverton - 1990 - How Many Species.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1257},
-pages = {293--304},
-title = {{How Many Species?}},
-url = {http://rstb.royalsocietypublishing.org/content/330/1257/293.abstract},
-volume = {330},
-year = {1990}
-}
-@article{Pancer-Koteja1998,
-abstract = {The response of a Rubus hirtus population to the creation of a new forest gap was analysed in a study conducted in Pinus sylvestris and Fagus sylvatica stands in the Ratanica Valley (Carpathian Foothills), Poland, during 1986-94. All individuals in two 30-m2 plots, one in a gap and one with full canopy cover, were mapped, and the length of Rubus shoots were measured 1, 2, 3, 4, and 7 years after the creation of the gap. Spatial patterns were analysed using Ripley's K-method. Although the density of Rubus in the gap increased from 3 to 24 rooting points/m2, the change in spatial pattern of individuals over 7 years was very limited. During the first four years, a clumped pattern appeared at distances of {\textgreater}0.5 m. However, after 7 years the pattern was random at all distances. Young shoots spread in all directions with equal probability. The expansion was achieved by the establishment of new ramets, with an increase in the number of shoots per rooting point playing a minor role. Individual plants contributed unequally to gap filling, and few of them produced many rooting points. The average size of canes and the proportion of tip-rooting canes were highest in the second year after the gap formation.},
-author = {Pancer-Koteja, Elzbieta and Szwagrzyk, Jerzy and Bodziarczyk, Jan},
-doi = {10.2307/3237041},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pancer-Koteja, Szwagrzyk, Bodziarczyk - 1998 - Small-scale spatial pattern and size structure of Rubus hirtus in a canopy gap.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {755--762},
-title = {{Small-scale spatial pattern and size structure of Rubus hirtus in a canopy gap}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3237041/abstract},
-volume = {9},
-year = {1998}
-}
-@article{Zadeh1965,
-abstract = {A fuzzy set is a class of objects with a continuum of grades of membership. Such a set is characterized by a membership (characteristic) function which assigns to each object a grade of membership ranging between zero and one. The notions of inclusion, union, intersection, complement, relation, convexity, etc., are extended to such sets, and various properties of these notions in the context of fuzzy sets are established. In particular, a separation theorem for convex fuzzy sets is proved without requiring that the fuzzy sets be disjoint.},
-author = {Zadeh, L.A.},
-doi = {10.1016/S0019-9958(65)90241-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zadeh - 1965 - Fuzzy sets.pdf:pdf},
-journal = {Information and Control},
-number = {3},
-pages = {338--353},
-title = {{Fuzzy sets}},
-volume = {8},
-year = {1965}
-}
-@article{Holt2006,
-abstract = {Community ecology is in a current state of creative ferment, stimulated by the development of neutral models of community organization. Here, I reflect on recent papers by Scheffer and van Nes, and by Gravel et al., which illuminate how neutrality can emerge from ecological and evolutionary processes, thus suggesting ways to unify neutral and niche perspectives.},
-author = {Holt, Robert D.},
-doi = {10.1016/j.tree.2006.08.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holt - 2006 - Emergent neutrality.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {10},
-pages = {531--3},
-title = {{Emergent neutrality}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/16901580},
-volume = {21},
-year = {2006}
-}
-@article{Strauss1975,
-abstract = {A number of tests are available for the null hypothesis that a set of points in a region are scattered randomly, but relatively little is known about forms for the alternative. It is shown that under certain assumptions, the most severe of which is of Markov type, the probability density of the points must be of a simple explicit form depending on a single clustering parameter. The estimation of the parameter is studied and illustrated with an example.},
-annote = {ISI Document Delivery No.: AM412
-Times Cited: 107
-Cited Reference Count: 4
-STRAUSS, DJ
-BIOMETRIKA TRUST},
-author = {Strauss, David J.},
-doi = {10.1093/biomet/62.2.467},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Strauss - 1975 - A Model for Clustering.pdf:pdf},
-journal = {Biometrika},
-number = {2},
-pages = {467--475},
-title = {{A Model for Clustering}},
-url = {http://biomet.oxfordjournals.org/content/62/2/467.short},
-volume = {62},
-year = {1975}
-}
-@article{Weir1984,
-abstract = {ormulae are given for estimators for the parameters F, $\theta$, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.},
-author = {Weir, B. S. and Cockerham, C. Clark},
-doi = {10.2307/2408641},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weir, Cockerham - 1984 - Estimating F-Statistics for the Analysis of Population Structure.pdf:pdf},
-journal = {Evolution},
-number = {6},
-pages = {1358--1370},
-title = {{Estimating F-Statistics for the Analysis of Population Structure}},
-url = {https://www.jstor.org/stable/2408641},
-volume = {38},
-year = {1984}
-}
-@article{Zhang2013a,
-abstract = {This paper establishes the asymptotic normality of an entropy estimator with an exponentially decaying bias on any finite alphabet. Furthermore, it is shown that the nonparametric estimator is asymptotically efficient.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Zhang, Zhiyi},
-doi = {10.1109/TIT.2012.2217393},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang - 2013 - Asymptotic normality of an entropy estimator with exponentially decaying bias.pdf:pdf},
-journal = {IEEE Transactions on Information Theory},
-number = {1},
-pages = {504--508},
-title = {{Asymptotic normality of an entropy estimator with exponentially decaying bias}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84871778138{\&}partnerID=40{\&}md5=8bf65958a59ad3a1d621de522b1dc3bd},
-volume = {59},
-year = {2013}
-}
-@article{Moustafa2013,
-abstract = {Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy–based diversity indices, or diversity indices for short, suffer from three problems. First, when computing the diversity for samples withdrawn from communities with different structures, diversity indices can easily yield non-comparable and hard to interpret results. Second, diversity indices impose weighting schemes on the species distributions that unnecessarily emphasize low abundant rare species, or erroneously identified ones. Third, diversity indices do not allow for comparing distributions against each other, which is necessary when a community has a well-known species' distribution. In this paper we propose a new general methodology based on information theoretic principles to quantify the species diversity of a community. Our methodology, comprised of two steps, naturally overcomes the previous mentioned problems, and yields comparable and easy to interpret diversity values. We show that our methodology retains all the functional properties of any diversity index, and yet is far more flexible than entropy–based diversity indices. Our methodology is easy to implement and is applicable to any community of interest.},
-author = {Abou-Moustafa, Karim T.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Abou-Moustafa - 2013 - Divergence Measures as Diversity Indices.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Divergence Measures as Diversity Indices}},
-volume = {1408.2863},
-year = {2013}
-}
-@article{Ottaviano1998,
-author = {Ottaviano, Gianmarco I. P. and Puga, Diego},
-doi = {10.1111/1467-9701.00160},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ottaviano, Puga - 1998 - Agglomeration in the global economy A survey of the new economic geography.pdf:pdf},
-journal = {The World Economy},
-number = {6},
-pages = {707--731},
-title = {{Agglomeration in the global economy: A survey of the new economic geography}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9701.00160/abstract},
-volume = {21},
-year = {1998}
-}
-@article{Sabatini2014,
-abstract = {Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests.},
-author = {Sabatini, Francesco Maria and Burrascano, Sabina and Tuomisto, Hanna and Blasi, Carlo},
-doi = {10.1371/journal.pone.0095244},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sabatini et al. - 2014 - Ground layer plant species turnover and Beta diversity in southern-European old-growth forests.pdf:pdf},
-journal = {PloS one},
-number = {4},
-pages = {e95244},
-title = {{Ground layer plant species turnover and Beta diversity in southern-European old-growth forests.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3991708{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {9},
-year = {2014}
-}
-@book{Fischer2014,
-abstract = {The Handbook of Regional Science is a multi-volume reference work providing a state-of-the-art knowledge on regional science composed by renowned scientists in the field. The Handbook is intended to serve the academic needs of graduate students, and junior and senior scientists in regional science and related fields, with an interest in studying local and regional socio-economic issues.},
-doi = {10.1007/978-3-642-23430-9},
-editor = {Fischer, Manfred M. and Nijkamp, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Unknown - 2014 - Handbook of Regional Science.pdf:pdf},
-isbn = {978-3-642-23429-3},
-publisher = {Springer},
-title = {{Handbook of Regional Science}},
-url = {http://link.springer.com/10.1007/978-3-642-23430-9},
-year = {2014}
-}
-@article{Chiu2014a,
-abstract = {It is difficult to accurately estimate species richness if there are many almost undetectable species in a hyper-diverse community. Practically, an accurate lower bound for species richness is preferable to an inaccurate point estimator. The traditional nonparametric lower bound developed by Chao (1984, Scandinavian Journal of Statistics 11, 265-270) for individual-based abundance data uses only the information on the rarest species (the numbers of singletons and doubletons) to estimate the number of undetected species in samples. Applying a modified Good-Turing frequency formula, we derive an approximate formula for the first-order bias of this traditional lower bound. The approximate bias is estimated by using additional information (namely, the numbers of tripletons and quadrupletons). This approximate bias can be corrected, and an improved lower bound is thus obtained. The proposed lower bound is nonparametric in the sense that it is universally valid for any species abundance distribution. A similar type of improved lower bound can be derived for incidence data. We test our proposed lower bounds on simulated data sets generated from various species abundance models. Simulation results show that the proposed lower bounds always reduce bias over the traditional lower bounds and improve accuracy (as measured by mean squared error) when the heterogeneity of species abundances is relatively high. We also apply the proposed new lower bounds to real data for illustration and for comparisons with previously developed estimators.},
-author = {Chiu, Chun-Huo and Wang, Yi-Ting and Walther, Bruno A. and Chao, Anne},
-doi = {10.1111/biom.12200},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu et al. - 2014 - An Improved Nonparametric Lower Bound of Species Richness via a Modified Good-Turing Frequency Formula.pdf:pdf},
-journal = {Biometrics},
-number = {3},
-pages = {671--682},
-title = {{An Improved Nonparametric Lower Bound of Species Richness via a Modified Good-Turing Frequency Formula}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/24945937},
-volume = {70},
-year = {2014}
-}
-@article{Thebault2006,
-abstract = {Recent theoretical and experimental work provides clear evidence that biodiversity loss can have profound impacts on functioning of natural and managed ecosystems and the ability of ecosystems to deliver ecological services to human societies. Work on simplified ecosystems in which the diversity of a single trophic level is manipulated shows that diversity can enhance ecosystem processes such as primary productivity and nutrient retention. Theory also strongly suggests that biodiversity can act as biological insurance against potential disruptions caused by environmental changes. However, these studies generally concern a single trophic level, primary producers for the most part. Changes in biodiversity also affect ecosystem functioning through trophic interactions. Here we review, through the analysis of a simple ecosystem model, several key aspects inherent in multitrophic systems that may strongly affect the relationship between diversity and ecosystem processes. Our analysis shows that trophic interactions have a strong impact on the relationships between diversity and ecosystem functioning, whether the ecosystem property considered is total biomass or temporal variability of biomass at the various trophic levels. In both cases, food-web structure and trade-offs that affect interaction strength have major effects on these relationships. Multitrophic interactions are expected to make biodiversity-ecosystem functioning relationships more complex and non-linear, in contrast to the monotonic changes predicted for simplified systems with a single trophic level.},
-author = {Thebault, E. and Loreau, Michel},
-doi = {10.1007/s11284-005-0127-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thebault, Loreau - 2006 - The relationship between biodiversity and ecosystem functioning in food webs.pdf:pdf},
-journal = {Ecological Research},
-number = {1},
-pages = {17--25},
-title = {{The relationship between biodiversity and ecosystem functioning in food webs}},
-url = {http://link.springer.com/article/10.1007/s11284-005-0127-9},
-volume = {21},
-year = {2006}
-}
-@book{Diggle2013,
-author = {Diggle, Peter J.},
-edition = {3rd Editio},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle - 2013 - Statistical Analysis of Spatial and Spatio-Temporal Point Patterns.pdf:pdf},
-isbn = {978-1-4665-6024-6},
-publisher = {Chapman and Hall/CRC},
-title = {{Statistical Analysis of Spatial and Spatio-Temporal Point Patterns}},
-year = {2013}
-}
-@article{Devictor2010,
-abstract = {Functional and phylogenetic diversity are increasingly quantified in various fields of ecology and conservation biology. The need to maintain diversity turnover among sites, so-called beta-diversity, has also been raised in theoretical and applied ecology. In this study, we propose the first comprehensive framework for the large-scale mapping of taxonomic, phylogenetic and functional diversity and of their respective turnover. Using high-resolution data on the spatial distribution and abundance of birds at a country scale, we disentangled areas of mismatches and congruencies between biodiversity components. We further revealed unequal representation of each component in protected areas: functional diversity was significantly under-represented whereas taxonomic diversity was significantly over-represented in protected areas. Our results challenge the use of any one diversity component as a surrogate for other components and stress the need to adopt an integrative approach to biodiversity conservation.},
-author = {Devictor, Vincent and Mouillot, David and Meynard, Christine and Jiguet, Fr{\'{e}}d{\'{e}}ric and Thuiller, Wilfried and Mouquet, Nicolas},
-doi = {10.1111/j.1461-0248.2010.01493.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Devictor et al. - 2010 - Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity the need for integrati.pdf:pdf},
-journal = {Ecology letters},
-number = {8},
-pages = {1030--40},
-title = {{Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/20545736},
-volume = {13},
-year = {2010}
-}
-@article{Borrajo2017,
-abstract = {In the point process context, kernel intensity estimation has been mainly restricted to exploratory analysis due to its lack of consistency. However the use of covariates has allow to design consistent alternatives under some restrictive assumptions. In this paper we focus our attention on de$\backslash$-fi$\backslash$-ning an appropriate framework to derive a consistent kernel intensity estimator using covariates, as well as a consistent smooth bootstrap procedure. For spatial point processes with covariates there is no specific bandwidth selector, hence, we define two new data-driven procedures specifically designed for this scenario: a rule-of-thumb and a plug-in bandwidth based on the bootstrap method previously introduced. A simulation study is accomplished to understand the behaviour of these procedures in finite samples. Finally, we apply the techniques to a real set of data made up of wildfires in Canada during June 2015, using meteorological information as covariates.},
-archivePrefix = {arXiv},
-arxivId = {1703.03213},
-author = {Borrajo, M. I. and Gonz{\'{a}}lez-Manteiga, W. and Mart{\'{i}}nez-Miranda, M. D.},
-eprint = {1703.03213},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borrajo, Gonz{\'{a}}lez-Manteiga, Mart{\'{i}}nez-Miranda - 2017 - Kernel intensity estimation, bootstrapping and bandwidth selection for inhomogeneo.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Kernel intensity estimation, bootstrapping and bandwidth selection for inhomogeneous point processes depending on spatial covariates}},
-url = {http://arxiv.org/abs/1703.03213},
-volume = {1703.03213},
-year = {2017}
-}
-@article{Leslie2011,
-abstract = {This article presents a new metric we label the colocation quotient (CLQ), a measurement designed to quantify (potentially asymmetrical) spatial association between categories of a population that may itself exhibit spatial autocorrelation. We begin by explaining why most metrics of categorical spatial association are inadequate for many common situations. Our focus is on where a single categorical data variable is measured at point locations that constitute a population of interest. We then develop our new metric, the CLQ, as a point-based association metric most similar to the cross-k-function and join count statistic. However, it differs from the former in that it is based on distance ranks rather than on raw distances and differs from the latter in that it is asymmetric. After introducing the statistical calculation and underlying rationale, a random labeling technique is described to test for significance. The new metric is applied to economic and ecological point data to demonstrate its broad utility. The method expands upon explanatory powers present in current point-based colocation statistics.},
-author = {Leslie, T. F. and Kronenfeld, B. J.},
-doi = {10.1111/j.1538-4632.2011.00821.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leslie, Kronenfeld - 2011 - The Colocation Quotient A New Measure of Spatial Association Between Categorical Subsets of Points.pdf:pdf},
-journal = {Geographical Analysis},
-number = {3},
-pages = {306--326},
-title = {{The Colocation Quotient: A New Measure of Spatial Association Between Categorical Subsets of Points}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.2011.00821.x/abstract},
-volume = {43},
-year = {2011}
-}
-@article{Tucker2015,
-abstract = {The $\beta$-null deviation measure, developed as a null model for $\beta$-diversity, is increasingly used in empirical studies to detect the underlying structuring mechanisms in communities (e.g. niche versus neutral and stochastic versus deterministic). Despite growing use, the ecological interpretation of the presence/absence and abundance-based versions of the $\beta$-null diversity measure have not been tested against communities with known assembly mechanisms, and thus have not been validated as an appropriate tool for inferring assembly mechanisms. Using a mechanistic model with known assembly mechanisms, we simulated replicate metacommunities and examined $\beta$-null deviation values 1) across a gradient of niche (species-sorting) to neutrally structured metacommunities, 2) through time, and 3) we compared the effect of changes in assembly mechanism on the performance of the $\beta$-null deviation measures. The impact of stochasticity on assembly outcomes was also considered. $\beta$-null deviation measures proved to be interpretable as a measure of niche or neutral assembly. However, the presence/absence version of the $\beta$-null deviation measure could not differentiate between niche and neutral metacommunities if demographic stochasticity were present. The abundance-based $\beta$-null deviation measure was successful in distinguishing between niche and neutral metacommunities and was robust to the presence of stochasticity, changes through time, and changing assembly mechanisms. However, we suggest that it is not robust to changing abundance evenness distributions or sampling of communities, and so its interpretation still requires some care. We encourage the testing of the assumptions behind null models for ecology and care in their application.},
-author = {Tucker, Caroline M. and Shoemaker, Lauren G. and Davies, Kendi F. and Nemergut, Diana and Melbourne, Brett A.},
-doi = {10.1111/oik.02803},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tucker et al. - 2016 - Differentiating between niche and neutral assembly in metacommunities using null models of $\beta$-diversity.pdf:pdf},
-journal = {Oikos},
-number = {6},
-pages = {778--789},
-title = {{Differentiating between niche and neutral assembly in metacommunities using null models of $\beta$-diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/oik.02803/full},
-volume = {125},
-year = {2016}
-}
-@article{Lineweaver1934,
-author = {Lineweaver, Hans and Burk, Dean},
-doi = {10.1021/ja01318a036},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lineweaver, Burk - 1934 - The Determination of Enzyme Dissociation Constants.pdf:pdf},
-journal = {Journal of the American Chemical Society},
-number = {3},
-pages = {658--666},
-title = {{The Determination of Enzyme Dissociation Constants}},
-url = {http://dx.doi.org/10.1021/ja01318a036},
-volume = {56},
-year = {1934}
-}
-@article{Herrera1978,
-abstract = {See, stats, and : https : / / www . researchgate . net / publication / 284381873 Amazon , Their Functioning Nutrients Article CITATIONS 133 READS 221 4 , including : Some : Isotopic Mangrove - MADAM Roberto Cl{\'{i}}nica 71 , 577 SEE Ernesto Venezuelan 234 , 753 SEE All . The .},
-author = {Herrera, R and Jordan, Carl F and Klinge, H and Medina, E},
-isbn = {0378-1844},
-issn = {0378-1844},
-journal = {Interciencia},
-number = {4},
-pages = {223--232},
-pmid = {459},
-title = {{Amazon ecosystems. Their structure and functioning with particular emphasis on nutrients}},
-volume = {3},
-year = {1978}
-}
-@article{Spasojevic2015,
-abstract = {1.Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional-trait composition of communities (functional $\beta$-diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales. 2.We examined how ITV contributes to functional $\beta$-diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across scales, we compared patterns of functional $\beta$-diversity across soil-resource and topographic gradients at three spatial grains and three spatial extents. To quantify the contribution of ITV to functional $\beta$-diversity, we compared patterns that included ITV in five traits (leaf area, specific leaf area, leaf water content, leaf toughness, and chlorophyll content) to patterns based on species-mean trait values. 3.Functional $\beta$-diversity that included ITV increased with spatial extent and decreased with spatial grain, suggesting stronger environmental filtering within spatially extensive landscapes that contain populations locally adapted to different habitats. In contrast, functional $\beta$-diversity based on species-mean trait values increased with spatial extent but did not change with spatial grain, suggesting weaker environmental filtering among larger communities which each contain a variety of habitats and locally adapted populations. 4.Synthesis. Although studies typically infer community assembly mechanisms from species-mean trait values, our study suggests that mean trait values may mask the strength of assembly mechanisms such as environmental filtering, especially in landscape-scale studies that encompass strong environmental gradients and locally adapted populations. Our study highlights the utility of integrating ITV into studies of functional $\beta$-diversity to better understand the ecological conditions under which trait variation within and among species contributes most strongly to patterns of biodiversity across spatial scales.},
-author = {Spasojevic, Marko J. and Turner, Benjamin L. and Myers, Jonathan A.},
-doi = {10.1111/1365-2745.12518},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Spasojevic, Turner, Myers - 2016 - When does intraspecific trait variation contribute to functional beta-diversity.pdf:pdf},
-journal = {Journal of Ecology},
-pages = {487--496},
-title = {{When does intraspecific trait variation contribute to functional beta-diversity?}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12518},
-volume = {104},
-year = {2016}
-}
-@article{Smith2014a,
-abstract = {Nature (2014). doi:10.1038/nature13687},
-archivePrefix = {arXiv},
-arxivId = {NIHMS150003},
-author = {Smith, Brian Tilston and McCormack, John E. and Cuervo, Andr{\'{e}}s M. and Hickerson, Michael J. and Aleixo, Alexandre and Cadena, Carlos Daniel and P{\'{e}}rez-Em{\'{a}}n, Jorge and Burney, Curtis W. and Xie, Xiaoou and Harvey, Michael G. and Faircloth, Brant C. and Glenn, Travis C. and Derryberry, Elizabeth P. and Prejean, Jesse and Fields, Samantha and Brumfield, Robb T.},
-doi = {10.1038/nature13687},
-eprint = {NIHMS150003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Smith et al. - 2014 - The drivers of tropical speciation.pdf:pdf},
-isbn = {0028-0836},
-issn = {14764687},
-journal = {Nature},
-number = {7527},
-pages = {406--409},
-pmid = {25209666},
-title = {{The drivers of tropical speciation}},
-volume = {515},
-year = {2014}
-}
-@article{Cailliez1983,
-abstract = {If d is a measure of dissimilarity on a finite set withn elements, the smallest positive constant c* such that d +c has an euclidean representation for all c ≥c* is shown to be the largest eigen-value of a matrix of size 2n.},
-author = {Cailliez, Francis},
-doi = {10.1007/BF02294026},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cailliez - 1983 - The analytical solution of the additive constant problem.pdf:pdf},
-journal = {Psychometrika},
-pages = {305--310},
-title = {{The analytical solution of the additive constant problem}},
-volume = {48},
-year = {1983}
-}
-@article{Davies1977,
-abstract = {The testing of the hypothesis that a point process is Poisson against a one-dimensional alternative is considered. The locally optimal test statistic is expressed as an infinite series of uncorrelated terms. These terms are shown to be asymptotically equivalent to terms based on the various orders of cumulant spectra. The efficiency of tests based on partial sums of these terms is found.},
-author = {Davies, Robert B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Davies - 1977 - Testing the Hypothesis That a Point Process Is Poisson.pdf:pdf},
-journal = {Advances in Applied Probability},
-number = {4},
-pages = {724--746},
-title = {{Testing the Hypothesis That a Point Process Is Poisson}},
-url = {http://www.jstor.org/stable/1426698},
-volume = {9},
-year = {1977}
-}
-@article{Burbea1982,
-author = {Burbea, Jacob and Rao, C. Radhakrishna},
-doi = {10.1016/0047-259X(82)90065-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Burbea, Rao - 1982 - Entropy differential metric, distance and divergence measures in probability spaces A unified approach.pdf:pdf},
-journal = {Journal of Multivariate Analysis},
-month = {dec},
-number = {4},
-pages = {575--596},
-title = {{Entropy differential metric, distance and divergence measures in probability spaces: A unified approach}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/0047259X82900653},
-volume = {12},
-year = {1982}
-}
-@article{Guimaraes2011,
-abstract = {A common problem with spatial economic concentration measures based on areal data (e.g., Gini, Herfindhal, entropy, and Ellison-Glaeser indices) is accounting for the position of regions in space. While they purport to measure spatial clustering, these statistics are confined to calculations within individual areal units. They are insensitive to the proximity of regions or to neighboring effects. Clearly, since spillovers do not recognize areal units, economic clusters may cross regional boundaries. Yet with current measures, any industrial agglomeration that traverses boundaries will be chopped into two or more pieces. Activity in adjacent spatial units is treated in exactly the same way as activity in far-flung, nonadjacent areas. This paper shows how popular measures of spatial concentration relying on areal data can be modified to account for neighboring effects. With a U.S. application, we also demonstrate that the new instruments we propose are easy to implement and can be valuable in regional analysis.},
-author = {Guimar{\~{a}}es, Paulo and Figueiredo, Oct{\'{a}}vio and Woodward, Douglas},
-doi = {10.1111/j.1467-9787.2011.00723.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guimar{\~{a}}es, Figueiredo, Woodward - 2011 - Accounting for neighboring effects in measures of spatial concentration.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {4},
-pages = {678--693},
-publisher = {Blackwell Publishing Inc},
-title = {{Accounting for neighboring effects in measures of spatial concentration}},
-url = {http://dx.doi.org/10.1111/j.1467-9787.2011.00723.x},
-volume = {51},
-year = {2011}
-}
-@article{Pavoine2010,
-abstract = {Biodiversity studies aim to explain spatiotemporal patterns of species distributions. We propose a new methodology in which trait diversity is measured by the quadratic entropy index, with distances among species calculated from differences among trait states. We show how this index of trait diversity can be decomposed among the nodes of a phylogenetic tree. The contribution to trait diversity of a particular node is equal to the trait diversity among the n groups of species descending from it multiplied by an abundance weight (either proportional to the number of descendant species or to their relative abundance). We developed three tests to characterize the phylogenetic pattern of trait diversity and evaluated our methodology with seven evolutionary models. The power of the tests was high and increased with the number of extant taxa and the number of traits analyzed. The Type I error analyses (erroneous rejection of true null hypotheses) suggested that our tests are neither too liberal nor too conservative. Species abundances were found to modify the phylogenetic signal in trait diversity if only a few species were abundant and if species abundances were correlated to their phylogenetic relatedness and/or their trait states. By comparing phylogenetic signals in trait diversity from the local to the metacommunity level, we explored the factors that structure butterfly trait diversity in calcareous grasslands of northern France and southern Belgium. We show that partial phylogenetic signal in traits combined with habitat filtering determined which species and lineages were able to co-occur locally. Interestingly, no phylogenetic signal was detected when measures of abundance were included in our analyses. For most species and clades, the abundance distribution among communities at the regional scale was random. Overall, studying trait diversity in a phylogenetic context allows the link between current local ecological processes and lineage-dependent historical evolutionary factors to be thoroughly investigated.},
-annote = {doi: 10.1890/09-1290.1},
-author = {Pavoine, Sandrine and Baguette, Michel and Bonsall, Michael B.},
-doi = {10.1890/09-1290.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Baguette, Bonsall - 2010 - Decomposition of trait diversity among the nodes of a phylogenetic tree.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {485--507},
-title = {{Decomposition of trait diversity among the nodes of a phylogenetic tree}},
-url = {http://dx.doi.org/10.1890/09-1290.1},
-volume = {80},
-year = {2010}
-}
-@incollection{Taillie1979,
-address = {Fairland, MD},
-author = {Taillie, Charles},
-booktitle = {Ecological Diversity in Theory and Practice},
-editor = {Grassle, J. Frederick and Patil, Ganapati P. and Smith, W. K. and Taillie, Charles},
-pages = {51--62},
-publisher = {International Cooperative Publishing House},
-title = {{Species equitability: a comparative approach}},
-year = {1979}
-}
-@article{Arbia2008,
-abstract = {In this paper we aim at identifying stylized facts in order to suggest adequate models for the co-agglomeration of industries in space. We describe a class of spatial statistical methods for the empirical analysis of spatial clusters. The main innovation of the paper consists in considering clustering for bivariate (rather than univariate) distributions. This allows uncovering co-agglomeration and repulsion phenomena between the different sectors. Furthermore we present empirical evidence on the pair-wise intra-sectoral spatial distribution of patents in Italy in 1990s. We identify some distinctive joint patterns of location between different sectors and we propose some possible economic interpretations.},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Quah, Danny},
-doi = {10.1007/s00181-007-0154-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia, Espa, Quah - 2008 - A class of spatial econometric methods in the empirical analysis of clusters of firms in the space.pdf:pdf},
-journal = {Empirical Economics},
-number = {1},
-pages = {81--103},
-title = {{A class of spatial econometric methods in the empirical analysis of clusters of firms in the space}},
-url = {http://dx.doi.org/10.1007/s00181-007-0154-1},
-volume = {34},
-year = {2008}
-}
-@article{Flores2006,
-abstract = {The influence of environmental conditions and distance to nearest conspecific adult was determined to explain the distribution of saplings of six tree species in a lowland rain forest of French Guiana. The six focal species were three anemochorous light-demanding non-pioneer species: Dicorynia guianensis, Qualea rosea, Tachigali melinonii, and three zoochorous shade-tolerant species: Bocoa prouacensis, Oxandra asbeckii, Pogonophora schomburgkiana. The study was conducted at the research station of Paracou on forest plots differing in past logging treatments. The description of local environment included a characterization of past disturbance intensity (N = 5 variables), current stand (N = 4) and canopy structure (N = 3). Zero Inflated Poisson models were calibrated for each species to explain sapling numbers according to environmental conditions and distance to the nearest conspecific adult. These models extend generalized multiple regression to the case of discrete data with many zero counts. Model predictions were consistent with species temperaments: as expected, saplings of the light-demanding species were found more in disturbed and open local conditions while more saplings of the shade-tolerant species survived in stable and dense places. Predicted establishment curves of saplings around adults showed contrasting behavior among the species and did not systematically match with a priori expectations. These results are discussed in relation with dispersal syndromes and known establishment patterns in forest regeneration. Both differences in species shade-tolerance in early regeneration stages and dispersal limitation proved to account for sapling distribution in the understorey.},
-annote = {doi: DOI: 10.1016/j.actao.2005.08.007},
-author = {Flores, Olivier and Gourlet-Fleury, Sylvie and Picard, Nicolas},
-doi = {10.1016/j.actao.2005.08.007},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Flores, Gourlet-Fleury, Picard - 2006 - Local disturbance, forest structure and dispersal effects on sapling distribution of light-deman.pdf:pdf},
-journal = {Acta Oecologica},
-number = {2},
-pages = {141--154},
-title = {{Local disturbance, forest structure and dispersal effects on sapling distribution of light-demanding and shade-tolerant species in a French Guianian forest}},
-url = {http://www.sciencedirect.com/science/article/pii/S1146609X05000962},
-volume = {29},
-year = {2006}
-}
-@article{Bulla1994,
-author = {Bulla, Luis},
-doi = {10.2307/3545713},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bulla - 1994 - An index of evenness and its associated diversity measure.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {167--172},
-title = {{An index of evenness and its associated diversity measure}},
-url = {http://www.jstor.org/stable/3545713},
-volume = {70},
-year = {1994}
-}
-@article{Trafimow2003,
-abstract = {Because the probability of obtaining an experimental finding given that the null hypothesis is true [p(F$\backslash$H0)] is not the same as the probability that the null hypothesis is true given a finding [p(H0$\backslash$F)], calculating the former probability does not justify conclusions about the latter one. As the standard null-hypothesis significance-testing procedure does just that, it is logically invalid (J. Cohen, 1994). Theoretically, Bayes's theorem yields p(H0$\backslash$F), but in practice, researchers rarely know the correct values for 2 of the variables in the theorem. Nevertheless, by considering a wide range of possible values for the unknown variables, it is possible to calculate a range of theoretical values for p(H0$\backslash$F) and to draw conclusions about both hypothesis testing and theory evaluation.},
-author = {Trafimow, David},
-doi = {10.1037/0033-295X.110.3.526},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Trafimow - 2003 - Hypothesis testing and theory evaluation at the boundaries surprising insights from Bayes's theorem.pdf:pdf},
-journal = {Psychological review},
-number = {3},
-pages = {526--535},
-title = {{Hypothesis testing and theory evaluation at the boundaries: surprising insights from Bayes's theorem.}},
-volume = {110},
-year = {2003}
-}
-@article{Gajdos2001,
-abstract = {La recherche d'une mesure objective des in{\'{e}}galit{\'{e}}s, sur le mod{\`{e}}le des mesures des grandeurs physiques est vaine: la mesure des in{\'{e}}galit{\'{e}}s d{\'{e}}pend, en effet, de l'opinion des membres de la soci{\'{e}}t{\'{e}} en mati{\`{e}}re de justice distributive. Il est donc souhaitable que les opinions qui sous-tendent les mesures des in{\'{e}}galit{\'{e}}s soient aussi explicites que possible. Nous nous attachons, dans cette note, ? pr{\'{e}}senter et ? discuter en d{\'{e}}tail les cons{\'{e}}quences des opinions sur lesquelles est susceptible de se fonder une mesure des in{\'{e}}galit{\'{e}}s. Nous distinguons deux classes d'indices d'in{\'{e}}galit{\'{e}}s, selon qu'ils respectent, ou non, l'axiome d'ind{\'{e}}pendance. Les premiers sont les indices ? la Atkinson-Kolm-Sen, et s'inscrivent dans le cadre du mod{\`{e}}le d'esp{\'{e}}rance d'utilit{\'{e}} de von Neumann et Morgenstern. Les second sont les indices de Gini, Gini g{\'{e}}n{\'{e}}ralis{\'{e}}s et Gini super-g{\'{e}}n{\'{e}}ralis{\'{e}}s, et s'inscrivent dans le cadre du mod{\`{e}}le d'esp{\'{e}}rance d'utilit{\'{e}} d{\'{e}}pendant du rang de Yaari ou de Quiggin. Les indices de Gini et ses g{\'{e}}n{\'{e}}ralisations permettent une description beaucoup plus fine des opinions en mati{\`{e}}re de justice redistributive que les indices ? la Atkinson-Kolm-Sen, puisqu'ils reposent sur des axiomes plus faibles. Ces indices semblent donc particuli{\`{e}}rement bien adapt{\'{e}}s pour {\'{e}}valuer l'ad{\'{e}}quation des politiques redistributives ? des objectifs en mati{\`{e}}re de justice sociale.},
-author = {Gajdos, Thibault},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gajdos - 2001 - Les fondements axiomatiques de la mesure des in{\'{e}}galit{\'{e}}s.pdf:pdf},
-journal = {Revue d'{\'{e}}conomie politique},
-number = {5},
-pages = {683--719},
-title = {{Les fondements axiomatiques de la mesure des in{\'{e}}galit{\'{e}}s}},
-url = {http://www.cairn.info/revue-d-economie-politique-2001-5-page-683.htm},
-volume = {111},
-year = {2001}
-}
-@article{Jost2010b,
-abstract = {Aim Differentiation of sites or communities is often measured by partitioning regional or gamma diversity into additive or multiplicative alpha and beta components. The beta component and the ratio of within-group to total diversity (alpha/gamma) are then used to infer the compositional differentiation or similarity of the sites. There is debate about the appropriate measures and partitioning formulas for this purpose. We test the main partitioning methods, using empirical and simulated data, to see if some of these methods lead to false conclusions, and we show how to resolve the problems that we uncover.Location South America, Ecuador, Orellana province, Rio Shiripuno.Methods We construct sets of real and simulated tropical butterfly communities that can be unambiguously ranked according to their degree of differentiation. We then test whether beta and similarity measures from the different partitioning approaches rank these datasets correctly.Results The ratio of within-group diversity to total diversity does not reflect compositional similarity, when the Gini2013Simpson index or Shannon entropy are used to measure diversity. Additive beta diversity based on the Gini2013Simpson index does not reflect the degree of differentiation between N sites or communities.Main conclusions The ratio of within-group to total diversity (alpha/gamma) should not be used to measure the compositional similarity of groups, if diversity is equated with Shannon entropy or the Gini2013Simpson index. Conversion of these measures to effective number of species solves these problems. Additive Gini2013Simpson beta diversity does not directly reflect the differentiation of N samples or communities. However, when properly transformed onto the unit interval so as to remove the dependence on alpha and N, additive and multiplicative beta measures yield identical normalized measures of relative similarity and differentiation.},
-annote = {10.1111/j.1472-4642.2009.00626.x},
-author = {Jost, Lou and DeVries, Philip J. and Walla, Thomas and Greeney, Harold and Chao, Anne and Ricotta, Carlo},
-doi = {10.1111/j.1472-4642.2009.00626.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost et al. - 2010 - Partitioning diversity for conservation analyses.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {1},
-pages = {65--76},
-title = {{Partitioning diversity for conservation analyses}},
-url = {http://dx.doi.org/10.1111/j.1472-4642.2009.00626.x},
-volume = {16},
-year = {2010}
-}
-@article{Ricotta2007a,
-abstract = {Ecologists have traditionally viewed $\beta$-diversity as the ratio between $\gamma$-diversity and average $\alpha$-diversity. More recently, an alternative way of partitioning diversity has been proposed for which $\beta$-diversity is obtained as the difference between $\gamma$-diversity and average $\alpha$-diversity. Although this additive model of diversity decomposition is generally considered superior to its multiplicative counterpart, in both models $\beta$-diversity is a formally derived quantity without any self-contained ecological meaning; it simply quantifies the diversity excess of $\gamma$-diversity with respect to average $\alpha$-diversity. Taking this excess as an index of $\beta$-diversity is a questionable operation. In this paper, we show that a particular family of $\alpha$-diversity measures, the most celebrated of which is Rao's quadratic entropy, can be adequately used for summarizing $\beta$-diversity. Our proposal naturally leads to a new additive model of diversity for which, given two or more sets of plots, overall plot-to-plot species variability can be additively partitioned into two non-negative components: average variability in species composition within each set of plots and the species variability between the set of plots. For conservation purposes, the suggested change of perspective in the summarization of $\beta$-diversity allows for a flexible analysis of spatial heterogeneity in ecological diversity so that different hierarchical levels of biotic relevance (i.e. from the genetic to the landscape level) can be expressed in a significant and consistent way. {\textcopyright} 2007 The Authors Journal compilation {\textcopyright} 2007 Blackwell Publishing Ltd.},
-annote = {Cited By (since 1996):12
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: DIDIF
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome 'La Sapienza', Piazzale Aldo Moro, 5, 00185, Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo and Marignani, Michela},
-doi = {10.1111/j.1472-4642.2007.00316.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Marignani - 2007 - Computing $\beta$-diversity with Rao's quadratic entropy A change of perspective.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {2},
-pages = {237--241},
-title = {{Computing $\beta$-diversity with Rao's quadratic entropy: A change of perspective}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33847338913{\&}partnerID=40{\&}md5=17787638ece8d6a3cfd5b18f83cbccca},
-volume = {13},
-year = {2007}
-}
-@article{Tokeshi1990,
-abstract = {(1) This work examines the theoretical framework of species abundance patterns and the practical problems of applying models to real data, with particular reference to communities with a relatively small number of closely related species. (2) An attempt is made to give logical coherence to a range of niche apportionment models, including some newly developed ones. Niche apportionment can be categorized through the sequential breakage process of total niche, including the MacArthur Broken-Stick model which has traditionally been envisaged as a simultaneous breakage model. (3) Five niche apportionment models, i.e. Geometric Series, Dominance Preemption, Random Fraction, MacArthur Fraction and Dominance Decay are contrasted to a model where no conventional niche apportionment is assumed, i.e. Random Assortment model which may relate to a highly dynamic community under a variable environment. In addition, Composite model is proposed which combines niche apportionment and random assortment. (4) Species-abundance data from a community of epiphytic chironomids were used to illustrate the analyses involving the seven models. Random Fraction and Random Assortment both successfully fitted the data based on the number of individuals, whereas only Random Assortment successfully fitted the biomass data. The epiphytic chironomid community is considered to represent a highly dynamic system which is not structured through the process of niche apportionment envisaged here. (5) Subtleties of analysis involving a model-fitting exercise are discussed.},
-author = {Tokeshi, Mutsunori},
-doi = {10.2307/5036},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tokeshi - 1990 - Niche Apportionment or Random Assortment Species Abundance Patterns Revisited.pdf:pdf},
-isbn = {00218790},
-issn = {00218790},
-journal = {Journal of Animal Ecology},
-number = {3},
-pages = {1129--1146},
-pmid = {19009},
-title = {{Niche Apportionment or Random Assortment: Species Abundance Patterns Revisited}},
-url = {http://www.jstor.org/stable/5036},
-volume = {59},
-year = {1990}
-}
-@article{Wagner2003,
-abstract = {Spatial structure in plant communities occurs in the forms of (1) single-species aggregation and dispersion patterns, (2) distance-dependent interactions between species, and (3) the response to the spatial structure of environmental conditions. Different methods deal with these components of spatial variation: geostatistical analysis reveals autocorrelation in a spatial sample; the variance of species richness has been used as an indicator for interspecific interactions due to niche limitation; and ordination techniques describe multispecies responses to environmental factors. Based on the mathematical properties of presence-absence data, it is shown how variogram modeling, the testing of interspecific associations, and multiscale ordination can be integrated using the same set of distance-dependent variance-covariance matrices (variogram matrix). The variogram matrix partitions the variance of community data into spatial components at the levels of the individual species, species composition, and species richness. It can be used to factor out the effects of single-species aggregation patterns, interspecific interactions, or environmental heterogeneity. The mathematical integration of traditionally unrelated methods increases the interpretability of variograms of plant communities, provides a spatial extension and an empirical null model for the variance test of species richness, and extends multiscale ordination to nonsystematic spatial samples. Beyond the individual applications, the variogram matrix provides a framework for a mathematical unification of geostatistics, multivariate data analysis, and the analysis of variance that may enable ecologists from a broad range of fields to incorporate spatial effects into their research and to integrate analyses across different levels of biological organization.},
-author = {Wagner, Helene H.},
-doi = {10.1890/0012-9658(2003)084[1045:SCIPCI]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wagner - 2003 - Spatial covariance in plant communities Integrating ordination, geostatistics, and variance testing.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1045--1057},
-title = {{Spatial covariance in plant communities: Integrating ordination, geostatistics, and variance testing}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2003)084{\%}5B1045:SCIPCI{\%}5D2.0.CO;2/abstract},
-volume = {84},
-year = {2003}
-}
-@article{Mouillot2013,
-abstract = {Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63{\%} and 98{\%} of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32{\%} and 89{\%} of such species are locally and regionally rare, respectively. Remarkably, 47{\%} of fish species and 55{\%} of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning},
-author = {Mouillot, David and Bellwood, David R. and Baraloto, Christopher and Chave, Jerome and Galzin, Rene and Harmelin-Vivien, Mireille and Kulbicki, Michel and Lavergne, Sebastien and Lavorel, Sandra and Mouquet, Nicolas and Paine, C. E. Timothy and Renaud, Julien and Thuiller, Wilfried},
-doi = {10.1371/journal.pbio.1001569},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouillot et al. - 2013 - Rare Species Support Vulnerable Functions in High-Diversity Ecosystems.PDF:PDF},
-journal = {PLoS Biology},
-number = {5},
-pages = {e1001569},
-title = {{Rare Species Support Vulnerable Functions in High-Diversity Ecosystems}},
-url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001569},
-volume = {11},
-year = {2013}
-}
-@article{Ricotta2005c,
-abstract = {Intuitively, a community composed of ecologically dissimilar taxa is more diverse than a community composed of more similar taxa. However, since traditional diversity indices such as Shannon's entropy or Simpson's diversity are computed solely from the relative abundances of a given species assemblage, they cannot account for ecological differences between species. There have been recent developments regarding the use of quadratic entropy, a diversity index that incorporates both species relative abundances and a measure of the pairwise ecological differences between species. In this paper we firstly show that under some specific circumstances quadratic entropy can be additively decomposed into $\alpha$- $\beta$- and $\gamma$-diversities, a property that renders it a desirable measure of diversity in the ecological practice. Next, we suggest a quick and simple method for obtaining a standardized version of quadratic entropy that may allow an easier interpretation of the resulting diversity values. {\textcopyright} 2005 Societ{\`{a}} Botanica Italiana.},
-annote = {Cited By (since 1996):2
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: GBOIA
-Language of Original Document: English
-Correspondence Address: Ricotta, C.; Department of Plant Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy; email: carlo.ricotta@uniroma1.it},
-author = {Ricotta, Carlo and Avena, Giancarlo C.},
-doi = {10.1080/11263500500158736},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Avena - 2005 - A 'fast-food approach' to the standardization of quadratic diversity.pdf:pdf},
-journal = {Plant Biosystems},
-number = {3},
-pages = {411--413},
-title = {{A 'fast-food approach' to the standardization of quadratic diversity}},
-url = {http://dx.doi.org/10.1080/11263500500158736},
-volume = {139},
-year = {2005}
-}
-@article{Balmford2003,
-abstract = {Most attempts to quantify the impact of humanity on nature and bring it to public attention have centred around estimates of extinction rates. Suggestions that these figures have been exaggerated are, in our view, misplaced, but extinction rate estimates do face other problems – inevitable uncertainty, an arguably weak link to economic value, and insensitivity to short-term change. We therefore look here at other large-scale measures of the changing state of nature, focusing on recent analyses of trends in population size, numbers of populations and habitat extent. In spite of being limited by sampling inadequacies, these data provide a sensi- tive short-term complement to the long-term perspec- tive gained from considering extinction rates that can be linked directly both to economic values and to public concerns. Although further work is needed on extinc- tion rates, we conclude that significant new emphasis should be placed on instituting broader, more systema- tic monitoring of habitats and populations.},
-author = {Balmford, Andrew and Green, Rhys E. and Jenkins, Martin},
-doi = {10.1016/S0169-5347(03)00067-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Balmford, Green, Jenkins - 2003 - Measuring the changing state of nature.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {7},
-pages = {326--330},
-title = {{Measuring the changing state of nature}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534703000673},
-volume = {18},
-year = {2003}
-}
-@article{Botta-Duk??t2015,
-abstract = {1. The quest for ‘assembly rules', that is the processes shaping the species composition of communities, is a cen- tral issue in community ecology. Nevertheless, so far there is no general agreement on a framework to detect assembly rules in real-life data: several key elements are still missing or heavily disputed, including the choice of the appropriate test statistic (e.g. functional diversity index) and randomization strategy for each major assembly process. 2. Simulation studies based on artificial communities can helptoexplore theusefulnessofdifferentapproaches in detecting assembly rules. Nevertheless, the currently dominant approach to simulate artificial communities (i.e. selecting species from a pool based solely on trait values) oversimplifies the complex processes involved in community assembly and thus fails to produce realistic patterns. Consequently, its value for testingmethodolo- gies is seriously limited. 3. In this study, we implemented a flexible, individual-based algorithmsimulating real-life community processes (individuals are born, survive, compete for resources, reproduce and die), to generate artificial species composi- tion data.With the help of this algorithm, we estimated the type I error rates and the statistical power of five different diversity indices (FRic, Rao's quadratic entropy, FEve, the variance of functional distances, and the variance of nearest-neighbour distances) in combination with three randomization strategies (randomization of trait values in the whole data set, within-plots and within the range of trait values occurring in each plot) for detecting two underlying assembly processes (habitat filtering and limiting similarity). We also tested the influ- ence of all adjustable simulation parameters on the simulation results in a sensitivity analysis framework. 4. The results of the sensitivity analysis show that the individual-based simulation framework proposed here can be used for creating artificial community data with realistic pattern of trait values. Based on the results, Rao's quadratic entropy performed best for detecting both habitat filtering (trait convergence) and limiting similarity (trait divergence). Functional richness may also be suitable for detect traiting convergence. Functional evenness and variance of nearest-neighbour distances, however, should not be used for finding assembly rules.},
-author = {Botta-Duk{\'{a}}t, Zolt{\'{a}}n and Cz{\`{u}}cz, B{\'{a}}lint},
-doi = {10.1111/2041-210X.12450},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Botta-Duk{\'{a}}t, Cz{\`{u}}cz - 2016 - Testing the ability of functional diversity indices to detect trait convergence and divergence using individ.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-pages = {114--126},
-title = {{Testing the ability of functional diversity indices to detect trait convergence and divergence using individual-based simulation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12450/abstract},
-volume = {7},
-year = {2016}
-}
-@article{Camarero1999,
-abstract = {We describe the structure and spatial pattern of a subalpine forest-alpine pasture ecotone dominated by mountain pine (Pinus uncinata) in the eastern Pyrenees. The disturbance history of the study area suggests an ecotone pattern affected by local and recent disturbances (e.g., grazing). A rectangular plot (30x100 m) was located crossing the ecotone with its longest side parallel to the slope. We measured the location (x and y coordinates) and several structural variables (basal diameter, diameter at breast height, height, crown radii, number of needle age-classes, estimated age-number of internodes in the stem) for each P. uncinata individual within the plot. P. uncinata living individuals were classified according to their size (adults, poles, saplings and seedlings) and growth-form (krummholz-shrubby multistemmed individuals). The type of substrate (rock, organic matter, soil) and cover of P. uncinata, shrubs and herbaceous plants were described quantitatively using transects parallel to the slope. The ecotone structure was described through: (i) point pattern (Ripley's K, bi- and univariate cases); and (ii) surface pattern analyses (omni- and unidirectional Moran correlograms). The studied ecotone showed a distribution of P. uncinata individuals aggregated in patches, the saplings being predominant. These spatial analyses indicated the size of these tree patches for several variables measured for trees located in the forest (e. g. 8-10 m for the estimated age). The estimated age of young individuals ({\textless}60 years old) was positively related with height and basal diameter. Regeneration showed two maxima (1965-67, 1973-77). A potential age-class of older individuals was also present (1941-57). Since 1975, regeneration has decreased exponentially. The shrubby- herbaceous community of the ecotone was dominated by Festuca spp. and Juniperus communis subsp. alpina. Dominant substrates were rocks and organic matter. No evident spatial structure for the richness of shrub and herbaceous species was found. However, two similar undisturbed ecotones (Ordesa, Tesso) showed a greater species richness, and a linear trend of decreasing species richness approaching the forest. In the case of Tesso, there was a patchy spatial structure of species richness imposed over the linear trend. In the studied ecotone, the dominance of shrubby-herbaceous species and the type of substrates changed across the ecotone depending on the timberline location, and the cover and number of dominant P. uncinata individuals (e.g., the substrates formed by organic matter dominated under the tree patches and in the forest). This spatial variability and the absence of a clear trend of decreasing species richness approaching the forest suggest the influence of tree patches on the shrubby-herbaceous community and/or the influence of local and recent disturbances. The influence of tree patches on their micro-environment and the existence of local disturbances should be considered in order to understand the responses of subalpine forest/alpine pasture ecotones to global change. Local and recent human disturbances (e.g., fire) can form tree patches, than can act later as favourable sites for recolonization.},
-annote = {En Espagnol},
-author = {Camarero, Jes{\'{u}}s Julio and Guti{\'{e}}rrez, Emilia},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Camarero, Guti{\'{e}}rrez, Fortin - 2000 - Spatial pattern of subalpine forest-alpine grassland ecotones in the Spanish Central Pyrenees.pdf:pdf},
-journal = {Ecolog{\'{i}}a},
-pages = {225--256},
-title = {{Spatial structure of a subalpine forest/alpine pasture ecotone in the Estanys de la Pera (Eastern Pyrenees) formed of clumps of trees}},
-volume = {13},
-year = {1999}
-}
-@article{Filipe2004,
-abstract = {The nature of pathogen transport mechanisms strongly determines the spatial pattern of disease and, through this, the dynamics and persistence of epidemics in plant populations. Up to recently, the range of possible mechanisms or interactions assumed by epidemic models has been limited: either independent of the location of individuals (mean-field models) or restricted to local contacts (between nearest neighbours or decaying exponenially with distance). Real dispersal processes are likely to lie between these two extremes, and many are well described by long-tailed contact kernels such as power laws. We investigate the effect of different spatial dispersal mechanisms on the spatio-temporal spread of disease epidemics by simulating a stochastic Susceptible-infective model motivated by previous data analyses. Both long-term stationary behaviour (in the presence of a control or recovery process) and transient behaviour (which varies widely within and between epidemics) are examined. We demonstrate the relationship between epidemic size and disease pattern (characterized by spatial autocorrelation), and its dependence on dispersal and infectivity parameters. Special attention is given to boundary effects, which can decrease disease levels significantly relative to standard, periodic geometries in cases of long-distance dispersal. We propose and test a definition of transient duration which captures the dependence of transients on dispersal mechanisms. We outline an analytical approach that represents the behaviour of the spatially-explicit model, and use it to prove that the epidemic size is predicted exactly by the mean-field model (in the limit of an infinite system) when dispersal is sufficiently long ranged (i.e. when the power-law exponent a less than or equal to 2). (C) 2003 Elsevier Ltd. All rights reserved.},
-annote = {Article},
-author = {Filipe, J. A. N. and Maule, M. M.},
-doi = {10.1016/S0022-5193(03)00278-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Filipe, Maule - 2004 - Effects of dispersal mechanisms on spatio-temporal development of epidemics.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {2},
-pages = {125--141},
-title = {{Effects of dispersal mechanisms on spatio-temporal development of epidemics}},
-url = {http://www.sciencedirect.com/science/article/pii/S0022519303002789},
-volume = {226},
-year = {2004}
-}
-@article{Harte2008,
-abstract = {The biodiversity scaling metrics widely studied in macroecology include the species–area relationship (SAR), the scale-dependent species–abundance distribution (SAD), the distribution of masses or metabolic energies of individuals within and across species, the abundance–energy or abundance–mass relationship across species, and the species-level occupancy distributions across space. We propose a theoretical framework for predicting the scaling forms of these and other metrics based on the state-variable concept and an analytical method derived from information theory. In statistical physics, a method of inference based on information entropy results in a complete macro-scale description of classical thermodynamic systems in terms of the state variables volume, temperature, and number of molecules. In analogy, we take the state variables of an ecosystem to be its total area, the total number of species within any specified taxonomic group in that area, the total number of individuals across those species, and the summed metabolic energy rate for all those individuals. In terms solely of ratios of those state variables, and without invoking any specific ecological mechanisms, we show that realistic functional forms for the macroecological metrics listed above are inferred based on information entropy. The Fisher log series SAD emerges naturally from the theory. The SAR is predicted to have negative curvature on a log–log plot, but as the ratio of the number of species to the number of individuals decreases, the SAR becomes better and better approximated by a power law, with the predicted slope z in the range of 0.14–0.20. Using the 3/4 power mass–metabolism scaling relation to relate energy requirements and measured body sizes, the Damuth scaling rule relating mass and abundance is also predicted by the theory. We argue that the predicted forms of the macroecological metrics are in reasonable agreement with the patterns observed from plant census data across habitats and spatial scales. While this is encouraging, given the absence of adjustable fitting parameters in the theory, we further argue that even small discrepancies between data and predictions can help identify ecological mechanisms that influence macroecological patterns.},
-author = {Harte, John and Zillio, Tommaso and Conlisk, Erin and Smith, Adam B.},
-doi = {10.1890/07-1369.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harte et al. - 2008 - Maximum entropy and the state-variable approach to macroecology.pdf:pdf},
-journal = {Ecology},
-number = {10},
-pages = {2700--2711},
-title = {{Maximum entropy and the state-variable approach to macroecology}},
-url = {http://doi.wiley.com/10.1890/07-1369.1},
-volume = {89},
-year = {2008}
-}
-@article{Matern1960,
-abstract = {This book was first published in 1960 as No. 5 of Volume 49 of Reports of the Forest Research Institute of Sweden. It was at the same time a doctor's thesis in mathematical statistics at Stockholm University. In the second edition, a number of misprints and other errors have been corrected. An author index and a subject index have been added. Finally, a new postscript comments on the later development of the subjects treated in the book. BERTIL MATERN March r¢6 Acknowledgements The completion of this thesis was facilitated through the generous assist­ ance of several persons and institutions. I would wish to express my sincere gratitude to my teacher, Professor HARALD CRAMtR, now chancellor of the Swedish universities, for his valuable help and encouragement. Sincere thanks are also offered to Professor ULF GRENANDER for kindly reading the first version of the manuscript and giving valuable advice. The thesis has been prepared during two widely separated periods. A preliminary draft of Ch. 2 was written in 1948, whereas the remaining parts were completed in 1959-1960. The work originates from problems which I discussed in a publication in 1947. The problems were assigned to me by Professor MANFRED NASLUND, former head of the Swedish Forest Research Institute, now governor of the province Norrbotten. It is a pleasure to acknowledge my gratefulness to Professor Naslund for his un­ remitting encouragement and interest in my work.},
-annote = {cit{\'{e}} par Stoyan 1987},
-author = {Mat{\'{e}}rn, Bertil},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mat{\'{e}}rn - 1960 - Spatial variation.pdf:pdf},
-journal = {Meddelanden fr{\aa}n Statens Skogsforskningsinstitut},
-number = {5},
-pages = {1--144},
-title = {{Spatial variation}},
-url = {http://www.springer.com/cn/book/9781461578925},
-volume = {49},
-year = {1960}
-}
-@article{Hart2016,
-abstract = {Abstract Although the effects of variation between individuals within species are traditionally ignored in studies of species coexistence, the magnitude of intraspecific variation in nature is forcing ecolo- gists to reconsider. Compelling intuitive arguments suggest that individual variation may provide a previously unrecognised route to diversity maintenance by blurring species-level competitive dif- ferences or substituting for species-level niche differences. These arguments, which are motivating a large body of empirical work, have rarely been evaluated with quantitative theory. Here we incorporate intraspecific variation into a common model of competition and identify three path- ways by which this variation affects coexistence: (1) changes in competitive dynamics because of nonlinear averaging, (2) changes in species' mean interaction strengths because of variation in underlying traits (also via nonlinear averaging) and (3) effects on stochastic demography. As a consequence of the first two mechanisms, we find that intraspecific variation in competitive ability increases the dominance of superior competitors, and intraspecific niche variation reduces species- level niche differentiation, both of which make coexistence more difficult. In addition, individual variation can exacerbate the effects of demographic stochasticity, and this further destabilises coexistence. Our work provides a theoretical foundation for emerging empirical interests in the effects of intraspecific variation on species diversity.},
-author = {Hart, Simon P. and Schreiber, Sebastian J. and Levine, Jonathan M.},
-doi = {10.1111/ele.12618},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hart, Schreiber, Levine - 2016 - How variation between individuals affects species coexistence.pdf:pdf},
-isbn = {1461-0248 (Electronic)$\backslash$r1461-023X (Linking)},
-issn = {14610248},
-journal = {Ecology Letters},
-number = {8},
-pages = {825--838},
-title = {{How variation between individuals affects species coexistence}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12618/abstract;jsessionid=2EABE14F05B58BE65D23AA75C71676B1.f03t01},
-volume = {19},
-year = {2016}
-}
-@article{Heller2009,
-annote = {Times Cited: 14},
-author = {Heller, R. and Siegismund, H. R.},
-doi = {10.1111/j.1365-294X.2009.04185.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Heller, Siegismund - 2009 - Relationship between three measures of genetic differentiation G(ST), D-EST and G'(ST) how wrong have we bee.pdf:pdf},
-journal = {Molecular Ecology},
-number = {10},
-pages = {2080--2083},
-title = {{Relationship between three measures of genetic differentiation G(ST), D-EST and G'(ST): how wrong have we been?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2009.04185.x/abstract},
-volume = {18},
-year = {2009}
-}
-@article{Studeny2011,
-abstract = {Growing concern about the fate of biodiversity, highlighted by the Convention on Biological Diversity's 2010 and 2020 targets for stemming biodiversity loss, has intensified interest in methods of assessing change in ecological communities through time. Biodiversity is a multivariate concept, which cannot be well-represented by a single measure. However, diversity profiles summarize the multivariate nature of multi-species datasets, and allow a more nuanced interpretation of biodiversity trends than unitary metrics. Here we introduce a new approach to diversity profiling. Our method is based on the knowledge that an ecological community is never completely even and uses this departure from perfect evenness as a novel and insightful way of measuring diversity. We plot our measure of departure as a function of a free parameter, to generate “evenness profiles”. These profiles allow us to separate changes due to dominant species from those due to rare species, and relate these patterns to shifts in overall di...},
-author = {Studeny, Angelika C. and Buckland, Stephen T. and Illian, Janine B. and Johnston, A. and Magurran, Anne E.},
-doi = {10.1890/ES10-00074.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Studeny et al. - 2011 - Goodness-of-fit measures of evenness a new tool for exploring changes in community structure.pdf:pdf},
-journal = {Ecosphere},
-number = {2},
-pages = {art.15},
-title = {{Goodness-of-fit measures of evenness: a new tool for exploring changes in community structure}},
-volume = {2},
-year = {2011}
-}
-@article{Szwagrzyk1990,
-abstract = {The existence of a relationship between the spatial pattern of trees and the distribution of young individuals beneath the canopy has been tested in the beech (Fagus sylvatica) and spruce (Picea abies) — fir (Abies alba) forests in the mountainous region, using two different methods. The first method was the analysis of spatial pattern of individuals, the second one was based on calculating sums of influences of all trees occurring within analysed plot on a given point on the forest floor. Results of spatial pattern analyses were surprisingly consistent: almost all mature trees and seedlings didplayed a random pattern of spatial arrangement. However, there is a clear, although statistically insignificant tendency towards uniformity of spatial pattern with increasing sizes of analysed trees. Results of comparing sums of influences on regularly distributed points with sums of influences on seedlings or saplings revealed no tendency in forest regeneration to concentrate in places, where the sums were smaller than the average for a plot. This, coupled with the dominance of random spatial pattern of trees, suggests, that viewed on a small spatial scale, influence of competition among forest trees on their spatial arrangement is obscured by other factors, which are not closely related to the distribution of individuals.},
-author = {Szwagrzyk, Jerzy},
-doi = {10.1007/BF00134431},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Szwagrzyk - 1990 - Natural regeneration of forest related to the spatial structure of trees A study of two forest communities in Western.pdf:pdf},
-journal = {Vegetatio},
-number = {1},
-pages = {11--22},
-title = {{Natural regeneration of forest related to the spatial structure of trees: A study of two forest communities in Western Carpathians, southern Poland}},
-url = {https://link.springer.com/article/10.1007/BF00134431},
-volume = {89},
-year = {1990}
-}
-@article{Pielou1962,
-abstract = {1. In an aggregated plant population, the pattern within high density patches may be regular owing to competition. Tests for pattern, applied to the whole population, will usually indicate only the overall aggregation, and will not reveal the localized regularity. 2. Evidence as to whether or not competition is taking place may be obtained by collecting a sample of the short plant-to-nearest-neighbour distances only. Such a truncated sample of distances may be compared with a truncated theoretical distribution. 3. Certain simplifying assumptions as to the form of the distribution of these distances may be made. It is then possible to estimate the minimum distance which must separate any pair of plants if both are to attain a definite size. 4. The test for interplant competition was applied to five natural populations of forest trees. Three gave clear evidence that competition was occurring, and for these the minimum interplant distances were estimated.},
-author = {Pielou, Evelyn C.},
-doi = {10.2307/2257448},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pielou - 1962 - The use of plant-to-neighbour distances for the detection of competition.pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {357--367},
-title = {{The use of plant-to-neighbour distances for the detection of competition}},
-url = {https://www.jstor.org/stable/2257448},
-volume = {50},
-year = {1962}
-}
-@article{McIntire2009,
-abstract = {The ecological processes that create spatial patterns have been examined by direct measurement and through measurement of patterns resulting from experimental manipulations. But in many situations, creating experiments and direct measurement of spatial processes can be difficult or impossible. Here, we identify and define a rapidly emerging alternative approach, which we formalize as "space as a surrogate" for unmeasured processes, that is used to maximize inference about ecological processes through the analysis of spatial patterns or spatial residuals alone. This approach requires three elements to be successful: a priori hypotheses, ecological theory and/or knowledge, and precise spatial analysis. We offer new insights into a long-standing debate about process-pattern links in ecology and highlight six recent studies that have successfully examined spatial patterns to understand a diverse array of processes: competition in forest-stand dynamics, dispersal of freshwater fish, movement of American marten, invasion mechanisms of exotic trees, dynamics of natural disturbances, and tropical-plant diversity. Key benefits of using space as a surrogate can be found where experimental manipulation or direct measurements are difficult or expensive to obtain or not possible. We note that, even where experiments can be performed, this procedure may aid in measuring the in situ importance of the processes uncovered through experiments.},
-author = {McIntire, Eliot J. B. and Fajardo, Alex},
-doi = {10.1890/07-2096.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McIntire, Fajardo - 2009 - Beyond description The active and effective way to infer processes from spatial patterns.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {46--56},
-title = {{Beyond description: The active and effective way to infer processes from spatial patterns}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/07-2096.1/abstract},
-volume = {90},
-year = {2009}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2001,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{Arr{\^{e}}t{\'{e}} du 18 octobre 2001 portant application du d{\'{e}}cret no 2000-815 du 25 ao{\^{u}}t 2000 relatif {\`{a}} l'am{\'{e}}nagement et {\`{a}} la r{\'{e}}duction du temps de travail dans la fonction publique de l'Etat au minist{\`{e}}re de l'agriculture et de la p{\^{e}}che}},
-url = {http://www.legifrance.gouv.fr/jo{\_}pdf.do?cidTexte=JORFTEXT000000590792},
-year = {2001}
-}
-@article{Poorter2006a,
-abstract = {The effect of irradiance on leaf construction costs, chemical composition, and on the payback time of leaves was investigated. To enable more generalized conclusions, three different systems were studied: top and the most-shaded leaves of 10 adult tree species in a European mixed forest, top leaves of sub-dominant trees of two evergreen species growing in small gaps or below the canopy in an Amazonian rainforest, and plants of six herbaceous and four woody species grown hydroponically at low or high irradiance in growth cabinets. Daily photon irradiance varied 3-6-fold between low- and high-light leaves. Specific leaf area (SLA) was 30-130{\%} higher at low light. Construction costs, on the other hand, were 1-5{\%} lower for low-irradiance leaves, mainly because low-irradiance leaves had lower concentrations of soluble phenolics. Photosynthetic capacity and respiration, expressed per unit leaf mass, were hardly different for the low- and high-light leaves. Estimates of payback times of the high-irradiance leaves ranged from 2-4 d in the growth cabinets, to 15-20 d for the adult tree species in the European forest. Low-irradiance leaves had payback times that were 2-3 times larger, ranging from 4 d in the growth cabinets to 20-80 d at the most shaded part of the canopy of the mixed forest. In all cases, estimated payback times were less than half the life span of the leaves, suggesting that even at time-integrated irradiances lower than 5{\%} of the total seasonal value, investment in leaves is still fruitful from a carbon-economy point of view. A sensitivity analysis showed that increased SLA of low-irradiance leaves was the main factor constraining payback times. Acclimation in the other five factors determining payback time, namely construction costs, photosynthetic capacity per unit leaf mass, respiration per unit leaf mass, apparent quantum yield, and curvature of the photosynthetic light-response-curve, were unimportant when the observed variation in each factor was examined.},
-author = {Poorter, Hendrik and Pepin, Steeve and Rijkers, Toon and de Jong, Yvonne and Evans, John R. and Korner, Christian},
-doi = {10.1093/jxb/erj002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Poorter et al. - 2006 - Construction costs, chemical composition and payback time of high- and low-irradiance leaves.pdf:pdf},
-journal = {Journal of Experimental Botany},
-number = {2},
-pages = {355--371},
-title = {{Construction costs, chemical composition and payback time of high- and low-irradiance leaves}},
-url = {https://doi.org/10.1093/jxb/erj002},
-volume = {57},
-year = {2006}
-}
-@article{NgoBieng2011,
-abstract = {Background Growth modelling of complex stands calls for the use of spatially explicit single-tree models. Such models require spatially explicit tree locations as the initial state to run simulations. Given the cost of such data, virtual forest stands, where tree locations are simulated, are generally used as the initial state. Purpose The purpose of this study was to present models for simulating the spatial structure of complex stands. It focused on mixed oak–Scots pine stands of the Orleans forest (France) and on the spatial structure of canopy trees. Methods The spatial structure of the oak–pine stands was modelled with appropriate point process models. The models consisted of a combination of Poisson, Neyman– Scott and Soft core. Simulation of the point process models was based on precise characterisation of the studied stands. Twenty-five 1-ha oak–pine plots were characterised by the Ripley function. The models were then fitted to the identified spatial structure to reproduce univariate and bivariate spatial patterns in each spatial type. Conclusion This paper provides an approach for general modelling of a spatial structure of a particular mixture and may be enriched by other point process models for other types of mixed stand.},
-author = {{Ngo Bieng}, Marie-Ange and Ginisty, Christian and Goreaud, Fran{\c{c}}ois},
-doi = {10.1007/s13595-011-0033-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ngo Bieng, Ginisty, Goreaud - 2011 - Point process models for mixed sessile forest stands.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {2},
-pages = {267--274},
-title = {{Point process models for mixed sessile forest stands}},
-volume = {68},
-year = {2011}
-}
-@article{Bennett2015,
-abstract = {Aim Approaches to calculating beta diversity ($\beta$) include classical measures based on alpha ($\alpha$) and gamma ($\gamma$) diversity, and multivariate distance-based measures. Species–area relationships cause measurements of $\gamma$ to vary, making comparisons of classical $\beta$ among regions contingent on sampling effort. A recent null-modelling approach has attempted to account for variation in $\gamma$ by calculating the degree to which $\beta$ deviates from a random expectation. Here, we clarify the mathematical links between classical and multivariate approaches to measuring $\beta$, to derive predictions regarding the reliability of classical, null-model and multivariate approaches. Next, we use four ecological datasets and simulated data to test the consistency of these approaches across sampling effort and $\gamma$. We focus on an issue that arises when making comparisons among regions, namely that even small changes to the area sampled can differentially increase measured $\gamma$ in each region, potentially causing artefacts in $\beta$ that are driven by methodology rather than biology. Innovation Comparisons among regions using classical and null-model measures change dramatically as sampling effort and $\gamma$ increase. This change is understood for classical $\beta$ because of species–area relationships, but not for null-model measures, making comparisons among regions impossible using the null-model approach. Multiple-site dissimilarity shows a similar sensitivity to $\gamma$ as classical measures. In contrast, pairwise multivariate distances show no systematic effect of sampling effort and $\gamma$: increasing the number of sample plots decreases variability but does not alter mean $\beta$. Main conclusions Multivariate pairwise distances are independent of sample size, offering the most robust comparison among regions. The widespread influence of sampling effort and $\gamma$ indicate that only scale-dependent measures of classical and multiple-site $\beta$ are comparable, whereas null-model $\beta$ may not be comparable among regions. However, in cases where $\gamma$ is well known, multiple-site dissimilarity metrics offer several advantages, and should be strongly considered.},
-author = {Bennett, Joseph R. and Gilbert, Benjamin},
-doi = {10.1111/geb.12413},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bennett, Gilbert - 2015 - Contrasting beta diversity among regions how do classical and distance-based approaches compare.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {3},
-pages = {368--377},
-title = {{Contrasting beta diversity among regions: how do classical and distance-based approaches compare?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12413/abstract},
-volume = {25},
-year = {2016}
-}
-@article{Krugman1996,
-abstract = {In the United States, many industries have a Silicon Valley-type geographic localization. In Europe, these same industries often have four or more major centers of production. This difference is presumably the result of the formal and informal trade bathers that have divided the European market. With the growing integration of that market, however, there is the possibility that Europe will develop an American-style economic geography. This paper uses a theoretical model of industrial localization to demonstrate this possibility, and to show the possible transition costs associated with this shift. Paul},
-author = {Krugman, Paul and Venables, Anthony J.},
-doi = {10.1016/0014-2921(95)00104-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Krugman, Venables - 1996 - Integration, specialization and adjustment.pdf:pdf},
-journal = {European Economic Review},
-number = {3-5},
-pages = {959--967},
-title = {{Integration, specialization and adjustment}},
-volume = {40},
-year = {1996}
-}
-@article{Weiher1998,
-abstract = {In order to find and define any assembly rules for communities, we must first investigate the patterns among species assemblages. We used a series of null models to test for patterns in wetland plant composition al the level of species, functional guilds, and traits. At the species level, we found significant checkerboard and nestedness patterns. Three functional guilds had some tendency to contribute a constant percentage to species richness, but after Bonferroni correction there was no significant pattern. Coexisting plant species showed no consistent overall pattern of morphological dispersion. However, when we considered each of 11 traits in turn, we found that 4 traits were overdispersed and 3 were underdispersed. Thus there are morphological assembly rules that constrain wetland plant community composition. These results reconcile contrasting views of community assembly. Communities can be simultaneously structured by a tension between two forces: abiotic external forces that constrain certain traits within limits and biotic internal forces that tend to keep coexisting species from being too similar. Because our sites vary along a fertility/disturbance gradient, we also investigated how trait dispersion varies in space. Trait dispersion increases with soil Fertility; soil phosphorus explains about 36{\%} of the variance in mean nearest neighbor distance. Species richness tends to decline with mean nearest neighbor distance, which contrasts with the general pattern for animal assemblages.},
-annote = {Weiher, E Clarke, GDP Keddy, PA},
-author = {Weiher, Evan and Clarke, G. D. Paul and Keddy, Paul A.},
-doi = {10.2307/3547051},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weiher, Clarke, Keddy - 1998 - Community assembly rules, morphological dispersion, and the coexistence of plant species.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {309--322},
-title = {{Community assembly rules, morphological dispersion, and the coexistence of plant species}},
-volume = {81},
-year = {1998}
-}
-@article{Kukuliac2016,
-abstract = {Distance-based methods are applied in various fields of research. In this paper, a new rela-tive distance-based method, the W function, is introduced. This method contributes to the assessment of spatial patterns of economic activities using the stochastic Monte Carlo simula-tion, and supplements the typology of distance-based methods recently drawn up by Marcon and Puech. The capability of the W function is compared with results from the Kd and the recently defined m function methods, which are widely used for monitoring the spatial distri-bution of economic activities by considering several theoretical and empirical examples. The W function appears to provide more precise estimations of the density of economic activities compared to the m and Kd functions, particularly in cases of complex patterns such as double clustered distribution. It also appears to provide a more accurate evaluation of dispersion.},
-author = {Kukulia{\v{c}}, Pavel and Hor{\'{a}}k, Jiř{\'{i}}},
-doi = {10.1111/gean.12120},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kukulia{\v{c}}, Hor{\'{a}}k - 2016 - W Function A New Distance-Based Measure of Spatial Distribution of Economic Activities.pdf:pdf},
-journal = {Geographical Analysis},
-number = {2},
-pages = {199--214},
-title = {{W Function: A New Distance-Based Measure of Spatial Distribution of Economic Activities}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/gean.12120/full},
-volume = {49},
-year = {2017}
-}
-@incollection{Blandin2014,
-abstract = {L'invasion fulgurante du mot « biodiversity » dans les sph{\`{e}}res scientifiques et politico-m{\'{e}}diatiques, apr{\`{e}}s la Conf{\'{e}}rence de Rio de Janeiro, en 1992, a pu faire croire {\`{a}} l'{\'{e}}mergence d'un nouveau domaine scientifique. En r{\'{e}}alit{\'{e}}, la question de la diversit{\'{e}} du monde vivant est constitutive de l'histoire naturelle depuis que celle-ci existe. Au cours du XXe si{\`{e}}cle, les {\'{e}}cologistes n'ont pas attendu la parution de l'ouvrage BioDiversity (Wilson {\&} Peter, 1988) pour r{\'{e}}fl{\'{e}}chir {\`{a}} la fa{\c{c}}on de rendre compte de la diversit{\'{e}} des esp{\`{e}}ces au sein des syst{\`{e}}mes {\'{e}}cologiques, pour s'interroger sur les processus de diversification et rechercher la signification fonctionnelle de cette diversit{\'{e}}. Cent ans apr{\`{e}}s la parution de On the Origin of Species by Means of Natural Selection, o{\`{u}} Darwin montrait toute l'importance des « variations », l'{\'{e}}cologue George E. Hutchinson publiait un article lumineux sur ce que l'on pourrait appeler l'{\'{e}}cologie de la diversification. D{\`{e}}s les ann{\'{e}}es 1950, et jusqu'au d{\'{e}}but des ann{\'{e}}es 1980, de nombreux scientifiques ont cherch{\'{e}} {\`{a}} mesurer ce qui {\'{e}}tait appel{\'{e}} la diversit{\'{e}} sp{\'{e}}cifique, et {\`{a}} la caract{\'{e}}riser par des formulations math{\'{e}}matiques, tandis que d'autres exploraient les relations entre cette diversit{\'{e}} et la stabilit{\'{e}} des syst{\`{e}}mes {\'{e}}cologiques, guid{\'{e}}s par l'intuition que des syst{\`{e}}mes plus diversifi{\'{e}}s devraient {\^{e}}tre plus stables. Pourtant, d{\`{e}}s 1971, Stuart H. Hurlbert affirmait qu'{\`{a}} force d'avoir {\'{e}}t{\'{e}} d{\'{e}}finie de fa{\c{c}}on vari{\'{e}}e et disparate, la diversit{\'{e}} sp{\'{e}}cifique {\'{e}}tait devenue un « non-concept ». Edward O. Wilson, en 1988, s'{\'{e}}tait gard{\'{e}} de proposer une d{\'{e}}finition pr{\'{e}}cise de la biodiversit{\'{e}}. Bien d'autres s'en charg{\`{e}}rent par la suite. R{\'{e}}p{\'{e}}tition de l'histoire ? Jacques Blondel {\'{e}}crivait en 1995 que le concept de « biodiversit{\'{e}} » n'{\'{e}}tait qu'une coquille vide. Est-ce {\`{a}} dire que la diversit{\'{e}} du vivant, m{\^{e}}me transform{\'{e}}e en « biodiversit{\'{e}} », n'est pas un concept scientifique ? L'analyse de travaux s'{\'{e}}chelonnant des ann{\'{e}}es 1950 aux ann{\'{e}}es 1980 permet de cerner les questionnements sur la diversit{\'{e}} des esp{\`{e}}ces auxquels se sont affront{\'{e}}s les {\'{e}}cologistes, et de voir comment ont interagi intuitions, constructions th{\'{e}}oriques et recherches empiriques. L'invention de la biodiversit{\'{e}} a-t-elle fait progresser la recherche ? Un regard sur quelques publications d'apr{\`{e}}s Rio permet d'{\'{e}}baucher une r{\'{e}}ponse.},
-address = {Paris},
-author = {Blandin, Patrick},
-booktitle = {La biodiversit{\'{e}} en question. Enjeux philosophiques, {\'{e}}thiques et scientifiques},
-chapter = {1},
-editor = {Casetta, Elena and Delord, Julien},
-pages = {31--68},
-publisher = {Editions Mat{\'{e}}riologiques},
-title = {{La diversit{\'{e}} du vivant avant (et apr{\`{e}}s) la biodiversit{\'{e}} : rep{\`{e}}res historiques et {\'{e}}pist{\'{e}}mologiques}},
-year = {2014}
-}
-@book{Dauphine1988,
-address = {Montpellier},
-author = {Dauphin{\'{e}}, Andr{\'{e}} and Voiron-Canicio, Christine},
-booktitle = {Collection Reclus Modes d'Emploi},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dauphin{\'{e}}, Voiron-Canicio - 1988 - Variogrammes et structures spatiales.pdf:pdf},
-pages = {1--56},
-publisher = {GIP Reclus},
-title = {{Variogrammes et structures spatiales}},
-volume = {12},
-year = {1988}
-}
-@article{Hammond1999,
-abstract = {It has long been argued that seed dispersal enhances recruitment in tropical trees by allowing offspring to 'escape' strong density/distance-dependent attack by insects, pathogens and rodents. Here we examined the effects of canopy openness and parent-offspring distance upon the frequency and timing of Chlorocardium rodiei seed attack and germination within a 15-ha plot of Guyanan tropical rain forest. Seeds were artificially dispersed beneath parent tries, in the understorey away from trees and in gaps. Analysing our data from an 85-week period of regular monitoring, we found that the main spatial gradients, canopy openness and distance to nearest adult conspecific, do not lead to differences in the final number of seeds attacked by infesting scolytid beetles or rodents, The timing of beetle attack, however, varied along the distance gradient and this difference affords seeds at further distances a 'window' in which to germinate and produce a seedling before attack. Canopy openness was not a good predictor of rooting success, but distance was strongly associated with root and shoot formation success and the mean time to shoot formation. There was a strong negative effect of distance on the likelihood of a seed being colonised by scolytid beetles prior to removal by rodents and shoot failure was strongly associated with prior infestation. We believe these results bring a key point to bear on the well-established notion of distance-dependent attack on seeds in tropical rainforests, viz. that seed characteristics (size, germination syndrome) and the timing of attack may be more important in explaining patterns of early seedling recruitment than distance. Our studies suggest that advantages accrued through dispersal in species like Chlorocardium will depend heavily on the 'race' between seed germination and attack. In the case of Chlorocardium, the 'race' can be lost at considerable distances due to its prolonged dormancy and the temporal fluctuations in fruitfall and rainfall which influence attack and germination. The results presented here suggest that the lag between seed attack and germination in tropical trees can regulate the influence of parent-offspring distance on cohort recruitment at this life history stage.},
-author = {Hammond, David S. and Brown, Valerie K. and Zagt, Roderick},
-doi = {10.1007/s004420050778},
-journal = {Oecologia},
-number = {2},
-pages = {208--218},
-title = {{Spatial and temporal patterns of seed attack and germination in a large-seeded neotropical tree species}},
-volume = {119},
-year = {1999}
-}
-@article{Bunker2005,
-abstract = {Tropical forest biodiversity is declining, but the resulting effects on key ecosystem services, such as carbon storage and sequestration, remain unknown. We assessed the influence of the loss of tropical tree species on carbon storage by simulating 18 possible extinction scenarios within a well-studied 50-hectare tropical forest plot in Panama, which contains 227 tree species. Among extinction scenarios, aboveground carbon stocks varied by more than 600{\%}, and biological insurance varied by more than 400{\%}. These results indicate that future carbon storage in tropical forests will be influenced strongly by future species composition. In},
-author = {Bunker, D. E. and DeClerck, F. and Bradford, J. C. and Colwell, Robert K. and Perfecto, I. and Phillips, Oliver L. and Sankaran, M. and Naeem, Shahid},
-doi = {10.1126/science.1117682},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bunker et al. - 2005 - Species loss and aboveground carbon storage in a tropical forest.pdf:pdf},
-journal = {Science},
-number = {5750},
-pages = {1029--1031},
-title = {{Species loss and aboveground carbon storage in a tropical forest}},
-url = {http://www.sciencemag.org/cgi/content/full/1117682/DC1 Materials},
-volume = {310},
-year = {2005}
-}
-@article{Peet1975,
-author = {Peet, Robert K.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peet - 1975 - Relative diversity indices.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {496--498},
-title = {{Relative diversity indices}},
-url = {http://www.jstor.org/stable/1934984},
-volume = {56},
-year = {1975}
-}
-@unpublished{Espa2010,
-abstract = {The spatial concentration of firms has long been a central issue in economics both under the theoretical and the applied point of view due mainly to the important policy implications. A popular approach to its measurement, which does not suffer from the problem of the arbitrariness of the regional boundaries, makes use of micro data and looks at the firms as if they were dimensionless points distributed in the economic space. However in practical circumstances the points (firms) observed in the economic space are far from being dimensionless and are conversely characterized by different dimension in terms of the number of employees, the product, the capital and so on. In the literature, the works that originally introduce such an approach (e.g. Arbia and Espa, 1996; Marcon and Puech, 2003) disregard the aspect of the different firm dimension and ignore the fact that a high degree of spatial concentration may result from both the case of many small points clustering in definite portions of space and from only few large points clustering together (e.g. few large firms). We refer to this phenomena as to clustering of firms and clustering of economic activities. The present paper aims at tackling this problem by adapting the popular K- function (Ripley, 1977) to account for the point dimension using the framework of marked point process theory (Penttinen, 2006). Keywords:},
-address = {Trento},
-author = {Espa, Giuseppe and Giuliani, Diego and Arbia, Giuseppe},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Espa, Giuliani, Arbia - 2010 - Weighting Ripley's K-function to account for the firm dimension in the analysis of spatial concentration.pdf:pdf},
-institution = {University of Trento},
-publisher = {Universit{\`{a}} di Trento},
-series = {Discussion Paper},
-title = {{Weighting Ripley's K-function to account for the firm dimension in the analysis of spatial concentration}},
-year = {2010}
-}
-@article{Rossi1992,
-abstract = {Geostatistics brings to ecology novel tools for the interpretation of spatial patterns of organisms, of the numerous environmental components with which they interact, and of the joint spatial dependence between organisms and their environment. The purpose of this paper is to use data from the ecological literature as well as from original research to provide a comprehensive and easily understood analysis of geostatistics' manner of modeling and methods. The traditional geostatistical tool, the variogram, a tool that is beginning to be used in ecology, is shown to provide an incomplete and misleading summary of spatial pattern when local means and variances change. Use of the non-ergodic covariance and correlogram provides a more effective description of lag-to-lag spatial dependence because the changing local means and variances are accounted for. Indicator transformations capture the spatial patterns of nominal ecological variables like gene frequencies and the presence/absence of an organism and of subgroups of a population like large or small individuals. Robust variogram measures are shown to be useful in data sets that contain many data outliers. Appropriate removal of outliers reveals latent spatial dependence and patterns. Cross-variograms, cross-covariances, and cross-correlograms define the joint spatial dependence between co-occurring organisms. The results of all of these analyses bring new insights into the spatial relations of organisms in their environment.},
-author = {Rossi, Richard E and Mulla, David J and Journel, Andre G and Franz, Eldon H},
-doi = {10.2307/2937096},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rossi et al. - 1992 - Geostatistical Tools for Modeling and Interpreting Ecological Spatial Dependence.pdf:pdf},
-journal = {Ecological Monographs},
-number = {2},
-pages = {277--314},
-title = {{Geostatistical Tools for Modeling and Interpreting Ecological Spatial Dependence}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/2937096/full},
-volume = {62},
-year = {1992}
-}
-@article{Fujita1997,
-abstract = {Les activit{\'{e}}s {\'{e}}conomiques sont r{\'{e}}parties tr{\`{e}}s in{\'{e}}galement sur le territoire. L'explication de ce fait, simple mais r{\'{e}}pandu, constitue {\`{a}} elle seule la question centrale de l'{\'{e}}conomie g{\'{e}}ographique. Les principales raisons expliquant l'agglom{\'{e}}ration des entreprises et/ou des m{\'{e}}nages sont regroup{\'{e}}es en trois cat{\'{e}}gories: (i) les externalit{\'{e}}s dans le cadre de la concurrence parfaite, (ii) les rendements croissants en situation de concurrence monopolistique et (iii) les interactions strat{\'{e}}giques associ{\'{e}}es {\`{a}} la concurrence spatiale. Quelques principes g{\'{e}}n{\'{e}}raux en sont d{\'{e}}duits expliquant l'organisation de l'espace {\'{e}}conomique. D'autres approches, anciennes ou nouvelles, sont {\'{e}}galement abord{\'{e}}es en fin d'article. /// Economic activities are unevenly distributed over space. Explaining this simple but widespread phenomenon is the main purpose of economic geography. The main reasons for the emergence of economic agglomerations are the following ones: (i) externalities in perfectly competitive markets; (ii) increasing returns in environments characterized by monopolistic competition; and (iii) strategic interactions among firms. A few general principles governing the organization of the space-economy are then discussed. Finally some alternative approaches are briefly analyzed.},
-author = {Fujita, Masahisa and Thisse, Jacques-Fran{\c{c}}ois},
-doi = {10.2307/20076050},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fujita, Thisse - 1997 - Economie G{\'{e}}ographique, Probl{\`{e}}mes anciens et nouvelles perspectives.pdf:pdf},
-journal = {Annales d'Economie et de Statistique},
-pages = {37--87},
-title = {{Economie G{\'{e}}ographique, Probl{\`{e}}mes anciens et nouvelles perspectives}},
-url = {https://www.jstor.org/stable/20076050},
-volume = {45},
-year = {1997}
-}
-@book{Oldeman1990,
-address = {Berlin, Heidelberg},
-author = {Oldeman, Roelof A. A.},
-doi = {10.1007/978-3-642-75211-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Oldeman - 1990 - Forests Elements of Silvology.pdf:pdf},
-isbn = {978-3-642-75213-1},
-publisher = {Springer},
-title = {{Forests: Elements of Silvology}},
-url = {http://link.springer.com/10.1007/978-3-642-75211-7},
-year = {1990}
-}
-@incollection{Yokozawa2003,
-author = {Yokozawa, M.},
-booktitle = {Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models},
-doi = {10.1007/978-4-431-65958-7_20},
-editor = {Sekimura, T and Noji, S and Ueno, N and Maini, P K},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hans Meinhardt (auth.), Toshio Sekimura D.Sc., Sumihare Noji D.Sc., Naoto Ueno Ph.D., Philip K. Maini Ph.D. (eds.)-Morphogenesis and Pat.pdf:pdf},
-pages = {237--246},
-publisher = {Springer-Verlag},
-title = {{The mode of competition and spatial pattern formation in plant communities}},
-url = {https://link.springer.com/chapter/10.1007{\%}2F978-4-431-65958-7{\_}20},
-year = {2003}
-}
-@article{Marcon2014,
-abstract = {The dbmss package for R provides an easy-to-use toolbox to characterize the spatial structure of point patterns. Our contribution presents the state of the art of distance-based methods employed in economic geography and which are also used in ecology. Topographic functions such as Ripley's K, absolute functions such as Duranton and Overman's Kd and relative functions such as Marcon and Puech's M are implemented. Their confidence envelopes (including global ones) and tests against counterfactuals are included in the package.},
-author = {Marcon, Eric and Traissac, St{\'{e}}phane and Puech, Florence and Lang, Gabriel},
-doi = {10.18637/jss.v067.c03},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon et al. - 2015 - Tools to Characterize Point Patterns dbmss for R.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {3},
-pages = {1--15},
-title = {{Tools to Characterize Point Patterns: dbmss for R}},
-url = {http://cran.r-project.org/package=dbmss http://www.jstatsoft.org/v67/c03/},
-volume = {67},
-year = {2015}
-}
-@book{Marcon2014d,
-abstract = {La biodiversit{\'{e}} peut {\^{e}}tre mesur{\'{e}}e de fa{\c{c}}on claire et rigoureuse en utilisant l'entropie phylog{\'{e}}n{\'{e}}tique. Cette mesure g{\'{e}}n{\'{e}}ralise les indices de diversit{\'{e}} classique, traduit clairement la correspondance entre l'entropie et la diversit{\'{e}} au sens strict, int{\`{e}}gre si n{\'{e}}cessaire la distance entre esp{\`{e}}ces, peut {\^{e}}tre d{\'{e}}compos{\'{e}}e et corrig{\'{e}}e des biais d'estimation. Sa transformation en diversit{\'{e}} au sens strict permet d'interpr{\'{e}}ter les valeurs sous une forme unique : un nombre {\'{e}}quivalent d'esp{\`{e}}ces et un nombre {\'{e}}quivalent de communaut{\'{e}}s. Le package entropart permet de calculer avec R la diversit{\'{e}} d'une m{\'{e}}ta-communaut{\'{e}} {\`{a}} partir de donn{\'{e}}es d'abondances et d'un arbre phylog{\'{e}}n{\'{e}}tique ou fonctionnel. D'autres mesures de diversit{\'{e}} sont pr{\'{e}}sent{\'{e}}es ici, d'autres encore peuvent {\^{e}}tre trouv{\'{e}}es dans la litt{\'{e}}rature. Elles ont en g{\'{e}}n{\'{e}}ral un moins bon support math{\'{e}}matique, surtout les mesures de diversit{\'{e}} $\beta$, ne peuvent pas {\^{e}}tre d{\'{e}}compos{\'{e}}es, corrig{\'{e}}es ou interpr{\'{e}}t{\'{e}}es. La diversit{\'{e}} de Hurlbert poss{\`{e}}de toutes ses propri{\'{e}}t{\'{e}}s et une correction tr{\`{e}}s efficace du biais d'estimation, mais elle n'est pas g{\'{e}}n{\'{e}}ralis{\'{e}}e {\`{a}} la diversit{\'{e}} phylog{\'{e}}n{\'{e}}tique. La recherche sur la mesure de la diversit{\'{e}} est tr{\`{e}}s active, ce document {\'{e}}volue donc r{\'{e}}guli{\`{e}}rement pour prendre en compte les avanc{\'{e}}es r{\'{e}}centes.},
-address = {Kourou, France},
-author = {Marcon, Eric},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon - 2017 - Mesures de la Biodiversit{\'{e}}.pdf:pdf},
-publisher = {UMR EcoFoG},
-title = {{Mesures de la Biodiversit{\'{e}}}},
-url = {https://hal-agroparistech.archives-ouvertes.fr/cel-01205813},
-year = {2017}
-}
-@article{Herault2007a,
-abstract = {Both niche and neutral theories have been suggested as potential frameworks for modelling biodiversity. Niche models assume that biological traits represent evolutionary adaptations and define individuals in terms of functional trade-offs. Neutral models assume that all individuals at a single trophic level are functionally equivalent on a per capita basis with respect to their birth, death, dispersal and speciation. The opinion of many researchers is that neutral and niche processes operate simultaneously to generate diversity without knowing how the unification of both models can be achieved. Recently, several theoretical papers have reported evidence on the evolutionary emergence of niche structures shaping the emergence of groups of similar species. In this way, an Emergent Group is defined as a set of species that have a similar functional niche owing to a convergent ecological strategy. Central to the Emergent Group concept are the assumptions of functional equivalence within and of functional divergence between Emergent Groups. Within an Emergent Group, species richness is subject to a zero-sum rule set by the balance between the rate of individual loss and of immigration. Between Emergent Groups, tradeoffs such as seed size/seedling competitivity, investment in reproductive system/investment in vegetative systems or competitive ability/predator invulnerability are cornerstones of the evolutionary divergence. Delineating Emergent Groups amounts to reaching a compromise between maximizing niche differentiation (i.e. maximizing differences in functional tradeoffs) between Emergent Groups and maximizing neutrality within Emergent Groups. Up to now, the Emergent Group concept has been mostly proposed by theoretical scientists but it should be tested by empirical ecologists. The way in which niche and neutral models could be combined provides a profitable opportunity for theoretical and empirical scientists to collaborate fruitfully.},
-author = {H{\'{e}}rault, Bruno},
-doi = {10.1016/j.ppees.2007.08.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/H{\'{e}}rault - 2007 - Reconciling niche and neutrality through the Emergent Group approach.pdf:pdf},
-journal = {Perspectives in Plant Ecology, Evolution and Systematics},
-number = {2},
-pages = {71--78},
-title = {{Reconciling niche and neutrality through the Emergent Group approach}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1433831907000327},
-volume = {9},
-year = {2007}
-}
-@article{Ghazoul2015,
-abstract = {Forest degradation is a global environmental issue, but its definition is problematic. Difficulties include choosing appropriate reference states, timescales, thresholds, and forest values. We dispense with many such ambiguities by interpreting forest degradation through the frame of ecological resilience, and with reference to forest dynamics. Specifically, we define forest degradation as a state of anthropogenically induced arrested succession, where ecological processes that underlie forest dynamics are diminished or severely constrained. Metrics of degradation might include those that reflect ecological processes shaping community dynamics, notably the regeneration of plant species. Arrested succession implies that management intervention is necessary to recover successional trajectories. Such a definition can be applied to any forest ecosystem, and can also be extended to other ecosystems. Forest degradation results in biodiversity loss, greenhouse gas emissions, and diminution of ecosystem goods and services, but scientists, practitioners, and policy-makers are unable to agree a framework for defining degradation. Forests are spatially and temporally dynamic, and this stymies the selection of appropriate reference states, timescales, and thresholds against which degradation might be determined. Degradation is often defined as reduced capacity to provide goods and services. This definition takes little account of forest resilience - the ability of a system to reorganize and recover following disturbance. Advances in describing and quantifying ecosystem functioning have been fundamental in understanding forest dynamics, and provide a promising framework by which degradation might be better understood and, ultimately, defined.},
-author = {Ghazoul, Jaboury and Burivalova, Zuzana and Garcia-Ulloa, John and King, Lisa A.},
-doi = {10.1016/j.tree.2015.08.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ghazoul et al. - 2015 - Conceptualizing Forest Degradation.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {10},
-pages = {622--632},
-title = {{Conceptualizing Forest Degradation}},
-url = {http://dx.doi.org/10.1016/j.tree.2015.08.001},
-volume = {30},
-year = {2015}
-}
-@article{Henderson2003,
-abstract = {Using panel data this paper estimates plant level production functions for machinery and high-tech industries that allow for scale externalities from other plants in the same industry locally and from the scale or diversity of local economic activity outside the own industry. The paper finds that the count of other own industry plants, representing a count of local information spillover sources, has strong productivity effects in high tech but not machinery industries. Single plant firms both benefit more from and generate greater external benefits than corporate plants, given their greater reliance on external environments. On dynamic externalities, high-tech single plant firms benefit also from the scale of past own industry activity. I find little evidence of economies from the diversity or scale of local economic activity outside the own industry.},
-author = {Henderson, J. Vernon},
-doi = {10.1016/S0094-1190(02)00505-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Henderson - 2003 - Marshall's scale economies.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {1},
-pages = {1--28},
-title = {{Marshall's scale economies}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119002005053},
-volume = {53},
-year = {2003}
-}
-@article{Venables1996,
-abstract = {This paper considers the locational choice of firms in an upstream and a downstream industry. Both industries are imperfectly competitive, with firms subject to increasing returns. There are transport costs between the two locations. Depending on the level of these costs there may be a single equilibrium with production diversified between locations, or multiple equilibria, some of which involve agglomeration at a single location. Typically the forces for agglomeration are greatest at intermediate levels of transport costs. Reducing these costs from a high to an intermediate level will cause agglomeration and consequent divergence of economic structure and income levels; reducing them to a low level may cause the industries to operate in both locations, bringing convergence of structure and income. Equilibrium locations of vertically linked industries. Available from: https://www.researchgate.net/publication/30522332{\_}Equilibrium{\_}locations{\_}of{\_}vertically{\_}linked{\_}industries [accessed May 27, 2017].},
-author = {Venables, Anthony J.},
-doi = {10.2307/2527327},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Venables - 1996 - Equilibrium locations of vertically linked industries.pdf:pdf},
-journal = {International Economic Review},
-number = {2},
-pages = {341--359},
-title = {{Equilibrium locations of vertically linked industries}},
-url = {http://www.jstor.org/stable/2527327},
-volume = {37},
-year = {1996}
-}
-@incollection{May1975,
-author = {May, Robert M.},
-booktitle = {Ecology and Evolution of Communities},
-editor = {Cody, M L and Diamond, J M},
-pages = {81--120},
-publisher = {Harvard University Press},
-title = {{Patterns of species abundance and diversity}},
-year = {1975}
-}
-@article{Tuomisto2011,
-abstract = {Meaningful quantification of species diversity requires that both ‘species' and ‘diversity' are unambiguously defined. Rigorous rules of nomenclature exist to ensure that each species has a single unique name, but the naming of concepts is much more variable. As a consequence, ‘diversity' has been defined in so many different ways that its ability to transfer accurate information has been compromised. This problem can be solved by defining ‘diversity' as the effective number of species (or other types of interest), and using the term ‘true diversity' to specify that this narrow concept is being used (analogously to using the term ‘true bugs' when adhering to a narrow circumscription of ‘bugs'). Other measures related to diversity (such as entropies and probabilities) continue to be useful, but they represent different phenomena and should therefore be referred to by different names. Total species diversity in a dataset can be partitioned into two components in several different ways. The components of a specific multiplicative partitioning can be called true alpha diversity and true beta diversity. When the partitioning is done in some other way, the resulting components are different and should be called by other names. For example, the beta component of additive partitioning does not equal true beta diversity, but can logically be called species turnover. All the phenomena that have been called ‘beta diversity' in the ecological literature have also been called by alternative unique names. Consequently, a consistent terminology is already available; only a general agreement to use it is lacking.},
-author = {Tuomisto, Hanna},
-doi = {10.1007/s00442-011-2128-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto - 2011 - Commentary do we have a consistent terminology for species diversity Yes, if we choose to use it.pdf:pdf},
-journal = {Oecologia},
-number = {4},
-pages = {903--911},
-title = {{Commentary: do we have a consistent terminology for species diversity? Yes, if we choose to use it}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs00442-011-2128-4},
-volume = {167},
-year = {2011}
-}
-@article{Olszewski2004,
-abstract = {Biodiversity can be divided into two aspects: richness (the number of species or other taxa in a community or sample) and evenness (a measure of the distribution of relative abundances of different taxa in a community or sample). Sample richness is typically evaluated using rarefaction, which normalizes for sample size. Evenness is typically summarized in a single value. It is shown here that Hurlbert's probability of interspecific encounter (A1), a commonly used sample-size independent measure of evenness, equals the slope of the steepest part of the rising limb of a rarefaction curve. This means that rarefaction curves provide information on both aspects of diversity. In addition, regional diversity (gamma) can be broken down into the diversity within local communities (alpha) and differences in taxonomic composition among local communities (beta). Beta richness is expressed by the difference between the composite rarefaction curve of all samples in a region with the collector's curve for the same samples. The differences of the initial slopes of these two curves reflect the beta evenness thanks to the relationship between rarefaction and Al. This relationship can be further extended to help interpret species-area curves (SAC's). As previous authors have described, rarefaction provides the null hypothesis of passive sampling for SAC's, which can be interpreted as regional collector's curves. This allows evaluation of richness and evenness at local and regional scales using a single family of well- established, mathematically related techniques.},
-author = {Olszewski, Thomas D.},
-doi = {10.1111/j.0030-1299.2004.12519.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Olszewski - 2004 - A unified mathematical framework for the measurement of richness and evenness within and among multiple communities.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {377--387},
-title = {{A unified mathematical framework for the measurement of richness and evenness within and among multiple communities}},
-volume = {104},
-year = {2004}
-}
-@article{Wright2006b,
-abstract = {Deforestation and habitat loss are widely expected to precipitate an extinction crisis among tropical forest species. Humans cause deforestation, and humans living in rural settings have the greatest impact on extant forest area in the tropics. Current human demographic trends, including slowing population growth and intense urbanization, give reason to hope that deforestation will slow, natural forest regeneration through secondary succession will accelerate, and the widely anticipated mass extinction of tropical forest species will be avoided. Here, we show that the proportion of potential forest cover remaining is closely correlated with human population density among countries, in both the tropics and the temperate zone. We use United Nations population projections and continent-specific relationships between both total and rural population density and forest remaining today to project future tropical forest cover. Our projections suggest that deforestation rates will decrease as population growth slows, and that a much larger area will continue to be forested than previous studies suggest. Tropical forests retracted to smaller areas during repeated Pleistocene glacial events in Africa and more recently in selected areas that supported large prehistoric human populations. Despite many caveats, these projections and observations provide hope that many tropical forest species will be able to survive the current wave of deforestation and human population growth. A strategy to preserve tropical biodiversity might include policies to improve conditions in tropical urban settings to hasten urbanization and preemptive conservation efforts in countries with large areas of extant forest and large projected rates of future human population growth. We hope that this first attempt inspires others to produce better models of future tropical forest cover and associated policy recommendations. La deforestaci{\'{o}}n y la p{\'{e}}rdida de h{\'{a}}bitat pueden precipitar una crisis de la extinci{\'{o}}n de especies del bosque tropical. El mayor impacto sobre los bosques tropicales existentes es la deforestaci{\'{o}}n y otras actividades por humanos que viven en las {\'{a}}reas rurales Las tendencias demogr{\'{a}}ficas humanas actuales sugieren que una reducci{\'{o}}n en el crecimiento de la poblaci{\'{o}}n y un aumento en la urbanizaci{\'{o}}n podr{\'{a}}n causar una reducci{\'{o}}n en la deforestaci{\'{o}}n, una aceleraci{\'{o}}n de la sucesi{\'{o}}n secundaria, y evitar la esperada extinci{\'{o}}n en masa de especies del bosque tropical. Aqu{\'{i}}, demostramos que la proporci{\'{o}}n del potencial de la cobertura del bosque restante est{\'{a}} correlacionada con la densidad demogr{\'{a}}fica humana entre pa{\'{i}}ses; esto es aplicable a las zonas tropicales y templadas. Usamos proyecciones de las Naciones Unidas sobre crecimiento poblacionales y las relaciones entre la densidad poblacional rural y el bosque existente para proyectar la cobertura del bosque tropical en el futuro. Nuestras proyecciones sugieren que las tasas de deforestaci{\'{o}}n disminuiran conjuntamente con una reducci{\'{o}}n en el crecimiento poblacional, y a la vez, {\'{a}}reas m{\'{a}}s extensas que los sugeridos en otros estudios permanecer{\'{a}}n con cobertura forestal. Los bosques tropicales se retraeron a {\'{a}}reas m{\'{a}}s peque{\~{n}}as durante los repetidos eventos glaciales del Pleistoceno en el Africa y m{\'{a}}s recientemente en {\'{a}}reas selectas ocupadas por grandes poblaciones humanas prehist{\'{o}}ricas. A pesar de muchas advertencias, estas proyecciones y observaciones dan la esperanza de que muchas especies del bosque tropical podr{\'{a}}n sobrevivir la presente tasa de deforestaci{\'{o}}n y crecimiento poblacional humano. Una estrategia para preservar la biodiversidad tropical puede incluir pol{\'{i}}ticas para mejorar las condiciones ambientales en {\'{a}}reas urbanas tropicales. Esto con el objectivo de acelerar la urbanizaci{\'{o}}n y programas de conservaci{\'{o}}n preventivos en pa{\'{i}}ses con {\'{a}}reas extensas de bosque con un alto {\'{i}}ndice de crecimiento poblacional projectado para el futuro. Esperamos que nuestro primer esfuerzo inspire a otros investigadores a producir mejores modelos para predecir la cobertura del bosque tropical y pol{\'{i}}ticas asociadas con la conservacion de estos.},
-author = {Wright, S. Joseph and Muller-Landau, Helene C.},
-doi = {10.1111/j.1744-7429.2006.00154.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright, Muller-Landau - 2006 - The Future of Tropical Forest Species.pdf:pdf},
-journal = {Biotropica},
-number = {3},
-pages = {287--301},
-title = {{The Future of Tropical Forest Species}},
-url = {http://dx.doi.org/10.1111/j.1744-7429.2006.00154.x},
-volume = {38},
-year = {2006}
-}
-@article{Menhinick1964,
-abstract = {A comparison was made of several cumulative species/cumulative individuals indices using a statistical distribution corresponding to the species of insects in a sample from the herb stratum of a lespedeza field. Criteria used in comparison were that the indices be intensive for a given universe regardless of sample size and that the indices differentiate between universes having different numbers of species for a given number of individuals. Speciesllog individuals, species-llnatural square root of individuals were examined. Only the index of specieslsquare root of individuals met both of the criteria.},
-author = {Menhinick, Edward F.},
-doi = {10.2307/1934933},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Menhinick - 1964 - A Comparison of Some Species-Individuals Diversity Indices Applied to Samples of Field Insects.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {859--861},
-title = {{A Comparison of Some Species-Individuals Diversity Indices Applied to Samples of Field Insects}},
-volume = {45},
-year = {1964}
-}
-@article{Chave2002,
-abstract = {To represent species turnover in tropical rain forest, we use a neutral model where a tree's fate is not affected by what species it belongs to, seeds disperse a limited distance from their parents, and speciation is in equilibrium with random extinction. We calculate the similarity function, the probability F(r) that two trees separated by a distance r belong to the same species, assuming that the dispersal kernel P(r), the distribution of seeds about their parents and the prospects of mortality and reproduction, are the same for all trees regardless of their species. If P(r) is radially symmetric Gaussian with mean-square dispersal distance r; FðrÞ can be expressed in closed form. If P(r) is a radially symmetric Cauchy distribution, then, in two-dimensional space, F(r) is proportional to 1=r for large r: Analytical results are compared with individual-based simulations, and the relevance to field observations is discussed.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Leigh, Egbert G.},
-doi = {10.1006/tpbi.2002.1597},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Leigh - 2002 - A Spatially Explicit Neutral Model of $\beta$-Diversity in Tropical Forests.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {2},
-pages = {153--168},
-title = {{A Spatially Explicit Neutral Model of $\beta$-Diversity in Tropical Forests}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580902915972},
-volume = {62},
-year = {2002}
-}
-@article{DAmen2017,
-abstract = {1.In this study, we compare two community modelling approaches to determine their ability to predict the taxonomic, functional and phylogenetic properties of plant assemblages along a broad elevation gradient and at a fine resolution. The first method is the standard stacking individual species distribution modelling (SSDM) approach, which applies a simple environmental filter to predict species assemblages. The second method couples the SSDM and macroecological modelling (MEM - SSDM-MEM) approaches to impose a limit on the number of species co-occurring at each site. Because the detection of diversity patterns can be influenced by different levels of phylogenetic or functional trees, we also examine whether performing our analyses from broad to more exact structures in the trees influences the performance of the two modelling approaches when calculating diversity indices. 2.We found that coupling the SSDM with the MEM improves the overall predictions for the three diversity facets compared with those of the SSDM alone. The accuracy of the SSDM predictions for the diversity indices varied greatly along the elevation gradient, and when considering broad to more exact structure in the functional and phylogenetic trees, the SSDM-MEM predictions were more stable. 3.SSDM-MEM moderately but significantly improved the prediction of taxonomic diversity, which was mainly driven by the corrected number of predicted species. The performance of both modelling frameworks increased when predicting the functional and phylogenetic diversity indices. In particular, fair predictions of the taxonomic composition by SSDM-MEM led to increasingly accurate predictions of the functional and phylogenetic indices, suggesting that the compositional errors were associated with species that were functionally or phylogenetically close to the correct ones; however, this did not always hold for the SSDM predictions. 4.Synthesis. In this study, we tested the use of a recently published approach that couples species distribution and macroecological models to provide the first predictions of the distribution of multiple facets of plant diversity: taxonomic, functional and phylogenetic. Moderate but significant improvements were obtained; thus, our results open promising avenues for improving our ability to predict the different facets of biodiversity in space and time across broad environmental gradients when functional and phylogenetic information is available.},
-author = {D'Amen, Manuela and Mateo, Rub{\'{e}}n G. and Pottier, Julien and Thuiller, Wilfried and Maiorano, Luigi and Pellissier, Lo{\"{i}}c and Ndiribe, Charlotte and Salamin, Nicolas and Guisan, Antoine},
-doi = {10.1111/1365-2745.12801},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/D'Amen et al. - 2017 - Improving spatial predictions of taxonomic, functional and phylogenetic diversity.pdf:pdf},
-journal = {Journal of Ecology},
-title = {{Improving spatial predictions of taxonomic, functional and phylogenetic diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12801/full},
-volume = {in press},
-year = {2017}
-}
-@incollection{Delord2014,
-abstract = {{\`{A}} l'heure o{\`{u}} les politiques de protection de la biodiversit{\'{e}} {\'{e}}chouent syst{\'{e}}matiquement {\`{a}} r{\'{e}}sorber son {\'{e}}rosion, il est temps de s'interroger sur les fondements philosophiques du concept de biodiversit{\'{e}}. En partant du sympt{\^{o}}me de la multiplication des d{\'{e}}finitions de la biodiversit{\'{e}}, nous analysons la nature floue de cette notion. En nous appuyant sur une analyse historique du concept de diversit{\'{e}} biologique, nous serons conduits {\`{a}} faire de la biodiversit{\'{e}} g{\'{e}}n{\'{e}}rale un concept-grappe dont la scientificit{\'{e}} est questionnable. Au contraire, nous assimilons les concepts de biodiversit{\'{e}} limit{\'{e}}s {\`{a}} des « sortes » th{\'{e}}oriques. Cette dualit{\'{e}} {\'{e}}pist{\'{e}}mologique inh{\'{e}}rente aux concepts de biodiversit{\'{e}} nous permet de conclure sur les faiblesses de la notion de biodiversit{\'{e}} relativement {\`{a}} son usage conservationniste.},
-address = {Paris},
-author = {Delord, Julien},
-booktitle = {La biodiversit{\'{e}} en question. Enjeux philosophiques, {\'{e}}thiques et scientifiques},
-chapter = {3},
-doi = {10.3917/edmat.delor.2014.01.0083},
-editor = {Casetta, Elena and Delord, Julien},
-pages = {83--118},
-publisher = {Editions Mat{\'{e}}riologiques},
-title = {{La biodiversit{\'{e}} : imposture scientifique ou ruse {\'{e}}pist{\'{e}}mologique ?}},
-url = {https://www.cairn.info/resume.php?ID{\_}ARTICLE=EDMAT{\_}DELOR{\_}2014{\_}01{\_}0083},
-year = {2014}
-}
-@article{Combes2000,
-abstract = {For 52 industry sectors and 42 services sectors, this paper tests how the local economic structure (local sectoral specialization and diversity, competition, average size of plants, and total employment density) affects the 1984–1993 employment growth of 341 local areas. These areas entirely and continuously cover the French territory. The impact of the local economic structure differs in industry and services. In industrial sectors, local total employment density, competition, and plant size always reduce local growth. Sectoral specialization and diversity have a negative impact on growth, but also increase the growth of a few sectors. Service sectors always exhibit negative specialization effects and positive diversity effects. Competition and plant size have a negative impact and density a positive one, but exceptions are observed for some sectors.},
-author = {Combes, Pierre-Philippe},
-doi = {10.1006/juec.1999.2143},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Combes - 2000 - Economic Structure and Local Growth France, 1984-1993.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {3},
-pages = {329--355},
-title = {{Economic Structure and Local Growth: France, 1984-1993}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119099921435},
-volume = {47},
-year = {2000}
-}
-@article{Pavoine2014,
-abstract = {Summary: Current developments of diversity measures that consider that species are not equivalent, concentrate on how functionally or phylogenetically (dis)similar species are from each other (interspecific components). To assess the biodiversity of a community, few of the developed measures include intraspecific components, that is to say components that concern only the current features of the individuals of a species or the history of the species regardless of the other extant species of the community. A requirement for new developments in diversity indices could thus be to integrate both interspecific and intraspecific components. The objectives of our study are to introduce a parametric index of diversity (qH), expressed as an effective number of species, which satisfies this requirement, and to analyse the diversity of order 2 (2H). In the particular case of equal intraspecific components for every species, 2H is a simple function of Rao's quadratic entropy. We introduce our new index family and demonstrate that the vectors of species' proportions that maximize 2H are not necessarily unique and may have zeros (removing species). Then, we apply our index to two case studies: a theoretical example of phylogenetic diversity analysis; and a real data set on the changes in diet diversity of bird communities along an altitudinal gradient. Using a theoretical phylogenetic tree, we demonstrate that a maximizing vector for 2H can be associated with measures of species' phylogenetic originality. Applied to bird communities in Tarentaise Valley, France, 2H describes a decline in diet diversity with altitude due to a higher proportion of invertebrates in the diets of birds that occur where rocks replace deciduous and evergreen bushes and trees. Related to recent developments of diversity study made in the field of ecology, our approach has the advantages of integrating functional or phylogenetic intraspecific and interspecific components, and species' proportions (e.g. relative abundance or biomass), and of being applicable to many different data sets and objectives. Applied to both phylogenetic and functional diversity, our approach can help decisions when prioritizing conservation actions. {\textcopyright} 2013 British Ecological Society.},
-annote = {Export Date: 28 February 2014
-Source: Scopus},
-author = {Pavoine, Sandrine and Izs{\'{a}}k, J{\'{a}}nos},
-doi = {10.1111/2041-210X.12142},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Izs{\'{a}}k - 2014 - New biodiversity measure that includes consistent interspecific and intraspecific components.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {2},
-pages = {165--172},
-title = {{New biodiversity measure that includes consistent interspecific and intraspecific components}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84893984063{\&}partnerID=40{\&}md5=58981e8f98ae16672b67035c43f438cb},
-volume = {5},
-year = {2014}
-}
-@phdthesis{Bonneu2009a,
-address = {Toulouse},
-author = {Bonneu, Florent},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonneu - 2009 - Processus poctuels spatiaux pour l'analyse du positionnement optimal et de la concentration.pdf:pdf},
-pages = {138},
-publisher = {Universit{\'{e}} de Toulouse I},
-title = {{Processus poctuels spatiaux pour l'analyse du positionnement optimal et de la concentration}},
-year = {2009}
-}
-@article{Barot2003,
-abstract = {A previous study of the spatial patterns of Borassus aethiopum (a humid savanna palm tree) led to the following predictions: H I. Trees and termite mounds positively influence all developmental stages; H2. There is intense competition between B. aethiopum juveniles; H3. Juvenile and seedling survival and growth rates are higher away from mother plants; H4. Mound positive effect overwhelms the effect of intraspecific competition for very young B. aethiopum individuals, the reverse applies to older, non-reproductive individuals. To test for these hypotheses the potential positive and negative neighbourhood effects were analysed. Progression of seedlings into the juvenile stage and juvenile growth were analysed through logistic regression models including the effects of four neighbourhood indices designed to model the respective influence of B. aethiopum juveniles and adults, trees and termite mounds. Statistical results explain the observed spatial pattern and reveal two main neighbourhood effects that influence both B. aethiopum juveniles and seedlings: a positive effect of mounds due to the fact that they constitute nutrient-rich soil patches, and a negative effect of juveniles due to intraspecific competition. Seedlings would be mostly affected by the mound positive effect, whereas juveniles would be mostly affected by competition.},
-author = {Barot, S{\'{e}}bastien and Gignoux, Jacques},
-doi = {10.1111/j.1654-1103.2003.tb02130.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barot, Gignoux - 2003 - Neighbourhood analysis in the savanna palm Borassus aethiopum interplay of intraspecific competition and soil(2).pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {1},
-pages = {79--88},
-title = {{Neighbourhood analysis in the savanna palm Borassus aethiopum: interplay of intraspecific competition and soil patchiness}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2003.tb02130.x/abstract},
-volume = {14},
-year = {2003}
-}
-@article{Jaramillo2010a,
-abstract = {Jaramillo, C., Hoorn, C., Silva, S. A. F., Leite, F., Herrera, F., Quiroz, L., Dino, R., et al. (2010). The origin of the modern Amazon rainforest : implications of the palynological and palaeobotanical record. Amazonia, Landscape and Species Evolution: A Look into the Past.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Jaramillo, Carlos and Hoorn, Carina and Silva, Silane a F and Leite, Fatima and Herrera, Fabiany and Quiroz, Luis and Dino, Rodolfo and Antonioli, Luzia},
-doi = {10.1002/9781444306408.ch19},
-eprint = {arXiv:1011.1669v3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaramillo et al. - 2010 - The origin of the modern Amazon rainforest implications of the palynological and paleobotanical record.pdf:pdf},
-isbn = {9781405181136},
-issn = {1098-6596},
-journal = {Amazonia, Landscape and Species Evolution: A Look into the Past},
-pages = {317--334},
-pmid = {25246403},
-title = {{The origin of the modern Amazon rainforest: implications of the palynological and paleobotanical record}},
-year = {2010}
-}
-@article{Ferris2015,
-abstract = {The soil provides a great variety of microhabitats for myriad organisms of different size, physiological activity, behavior and ecosystem function. Besides abundance of participating soil organisms, their species diversity facilitates maximum exploitation of the resources available in the different habitats. At various levels of resolution, species can be categorized into classes performing ecosystem functions and, within each functional class, into guilds of species with similar life course characteristics. Measurement of the diversity and abundance of species within a functional class provides insights into the nature of ecosystem functions and services and to the health of the soil. At higher resolution, species diversity within guilds of a functional class may infer the degree of exploitation of available resources and the complementarity of an ecosystem service; diversity among the guilds of a functional class may indicate successional complementarity of the services. A diversity of guilds within a functional class expands the range of conditions over which ecosystem services are performed while species diversity within a functional class and its guilds contributes to the magnitude of the services. Consequently, diversity of species within functional classes is a key element of the biological component of soil health. In the context of ecosystem services and soil health, the biomass or metabolic activity of species are more useful measures of their abundance than numbers of individuals. Thus, understanding of soil health and ecosystem function requires, besides knowledge of species diversity within functional classes, assessment of the range of functions currently performed in the system and the abundances of organisms by which they are performed. We propose a diversity-weighted abundance product for comparison of the functional magnitude of different assemblages of like organisms.},
-author = {Ferris, Howard and Tuomisto, Hanna},
-doi = {10.1016/j.soilbio.2015.02.037},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ferris, Tuomisto - 2015 - Unearthing the role of biological diversity in soil health.pdf:pdf},
-journal = {Soil Biology and Biochemistry},
-pages = {101--109},
-title = {{Unearthing the role of biological diversity in soil health}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0038071715000917},
-volume = {85},
-year = {2015}
-}
-@article{Norden2009,
-abstract = {Understanding the recovery dynamics of ecosystems presents a major challenge in the human-impacted tropics. We tested whether secondary forests follow equilibrium or non-equilibrium dynamics by evaluating community reassembly over time, across different successional stages, and among multiple life stages. Based on long-term and static data from six 1-ha plots in NE Costa Rica, we show that secondary forests are undergoing reassembly of canopy tree and palm species composition through the successful recruitment of seedlings, saplings, and young trees of mature forest species. Such patterns were observed over time within sites and across successional stages. Floristic reassembly in secondary forests showed a clear convergence with mature forest community composition, supporting an equilibrium model. This resilience stems from three key factors co-occurring locally: high abundance of generalist species in the regional flora, high levels of seed dispersal, and local presence of old-growth forest remnants.},
-author = {Norden, Natalia and Chazdon, Robin L. and Chao, Anne and Jiang, Yi Huei and V{\'{i}}lchez-Alvarado, Braulio},
-doi = {10.1111/j.1461-0248.2009.01292.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Norden et al. - 2009 - Resilience of tropical rain forests Tree community reassembly in secondary forests.pdf:pdf},
-journal = {Ecology Letters},
-number = {5},
-pages = {385--394},
-title = {{Resilience of tropical rain forests: Tree community reassembly in secondary forests}},
-volume = {12},
-year = {2009}
-}
-@article{Cuzick1990,
-abstract = {A new method for detecting spatial clustering of events in populations with non-uniform density is proposed. The method is based on selecting controls from the population at risk and computing interpoint distances for the combined sample. Nonparametric tests are developed which are based on the number of cases among the k nearest neighbours of each case and the number of cases nearer than the k nearest control. The performance of these tests is evaluated analytically and by simulation and the method is applied to a data set on the locations of cases of childhood leukaemia and lymphoma in a defined geographical area. In particular the impact on power of the choice of k and of the ratio of cases to controls is examined. Modifications of the procedure to study distances from predefined objects, to match for known risk factors which would produce unwanted clustering and issues related to estimation are also discussed.},
-annote = {D{\'{e}}finition de Tk},
-author = {Cuzick, Jack and Edwards, Robert},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cuzick, Edwards - 1990 - Spatial Clustering for Inhomogeneous Populations.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {73--104},
-title = {{Spatial Clustering for Inhomogeneous Populations}},
-volume = {52},
-year = {1990}
-}
-@article{Newman2006,
-abstract = {Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.},
-author = {Newman, Mej},
-doi = {10.1073/pnas.0601602103},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Newman - 2006 - Modularity and community structure in networks.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {23},
-pages = {8577--82},
-title = {{Modularity and community structure in networks}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1482622{\&}tool=pmcentrez{\&}rendertype=abstract{\%}5Cnhttp://www.pnas.org/content/103/23/8577.short},
-volume = {103},
-year = {2006}
-}
-@incollection{Marcon2005,
-address = {Paris, France},
-author = {Marcon, Eric and Mucchielli, Jean-Louis and Puech, Florence},
-booktitle = {Localisation des activit{\'{e}}s et strat{\'{e}}gies de l'{\'{e}}tat - Rapport du commissariat g{\'{e}}n{\'{e}}ral du plan Groupe Perroux},
-editor = {Mouhoud, El Mouhoub},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Mucchielli, Puech - 2005 - Concentration g{\'{e}}ographique de l'emploi industriel et dynamiques territoriales en France de 1993 {\`{a}} 200.pdf:pdf},
-pages = {99--109},
-publisher = {L'Action Municipale},
-title = {{Concentration g{\'{e}}ographique de l'emploi industriel et dynamiques territoriales en France de 1993 {\`{a}} 2001}},
-year = {2005}
-}
-@article{Duranton1997,
-abstract = {{\`{A}} la crois{\'{e}}e des chemins du commerce international, de l'{\'{e}}conomie urbaine et de la micro-{\'{e}}conomie spatiale, la nouvelle {\'{e}}conomie g{\'{e}}ographique cherche {\`{a}} s'imposer comme un champ d'analyse distinct. Pour {\'{e}}valuer son {\'{e}}tat d'avancement, cet article effectue une synth{\`{e}}se sur la probl{\'{e}}matique de l' agglom{\'{e}}ration et la dispersion des activit{\'{e}}s et des personnes. Les r{\'{e}}ponses propos{\'{e}}es peuvent s'organiser suivant diff{\'{e}}rentes perspectives. Ainsi, les th{\'{e}}ories existantes se focalisent sur une ou plusieurs des trois dimensions principales du probl{\`{e}}me (taille, fonctions et les localisations des agglom{\'{e}}rations). Une autre partition est possible selon une dichotomie facteurs de proximit{\'{e}}/forces de longue distance. L'axe d'analyse choisi ici est toutefois historique : les diff{\'{e}}rentes sources d'agglom{\'{e}}ration et de dispersion agissent avec des intensit{\'{e}}s diff{\'{e}}rentes selon l'{\'{e}}tat du d{\'{e}}veloppement {\'{e}}conomique.},
-author = {Duranton, Gilles},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton - 1997 - La Nouvelle Economie G{\'{e}}ographique Agglom{\'{e}}ration et Dispersion.pdf:pdf},
-journal = {Economie et Pr{\'{e}}vision},
-number = {5},
-pages = {1--24},
-title = {{La Nouvelle Economie G{\'{e}}ographique: Agglom{\'{e}}ration et Dispersion}},
-url = {http://www.persee.fr/doc/ecop{\_}0249-4744{\_}1997{\_}num{\_}131{\_}5{\_}5882},
-volume = {131},
-year = {1997}
-}
-@article{Margalef1958,
-author = {Margalef, Ramon},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Margalef - 1958 - Information theory in ecology.pdf:pdf},
-journal = {General Systematics},
-pages = {36--71},
-title = {{Information theory in ecology}},
-volume = {3},
-year = {1958}
-}
-@article{Routledge1979,
-abstract = {Many indices have been proposed for measuring diversity. If we demand that any index satisfy a few basic properties, including that it contain hierarchical components, then only the subset, {\{}Na for a {\textgreater} 0{\}} of Hill's family need be considered. (This subset includes indices related to the Shannon-Wiener index, H{\^{a}}€² = log N1, and Simpson's index of concentration, {\^{I}}» = 1/N2.) Ecological components can also be defined for any of these indices. Only N2, however, can be used consistently to define local diversity and segregation components. These observations suggest that N2 is the best, single measure of diversity, and that the only other index worth considering is N1 .},
-annote = {doi: 10.1016/0022-5193(79)90015-8},
-author = {Routledge, R. D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Routledge - 1979 - Diversity indices Which ones are admissible.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {4},
-pages = {503--515},
-title = {{Diversity indices: Which ones are admissible?}},
-url = {http://www.sciencedirect.com/science/article/pii/0022519379900158},
-volume = {76},
-year = {1979}
-}
-@article{Rejou-Mechain2011,
-abstract = {1.In tropical forests, species distribution patterns may be strongly context-dependent owing to local stochasticity of recruitment and/or to the specific history and environment of each site. Recent studies have reported, however, that the degree of spatial aggregation of tropical tree species is partly determined by some species traits irrespectively of site conditions, at least at a very local scale ({\textless}200 m). 2.Here, we used standardized large-scale forest inventories of five Central African tropical forests (9670 0.5-ha plots spread over 5550 km²) to quantify the spatial aggregation of 106 tropical tree species at larger spatial scales. For this purpose, we developed a new statistic to quantify the respective contributions of different spatial scales to the aggregation patterns, and we tested whether patterns were consistent across sites. We finally asked whether species characteristics related to dispersal ability, to response to disturbances and to biogeographical range could significantly explain aggregation patterns. 3.Although aggregation patterns varied substantially among sites within each species, they displayed inter-site consistencies (21–24{\%} of the total variance explained by species identity) at the local scale (0.2–1 km) and at the mesoscale (1–10 km) but not at the landscape scale ({\textgreater}10 km). At the two former scales, upper taxonomical levels (family and/or order) significantly explained variation in the degree of species aggregation, while at the landscape scale, aggregation was entirely contingent on the site considered. Few species characteristics, except dispersal syndromes and wood density, were able to significantly explain aggregation patterns. 4.Synthesis. One of our most striking results is the high context dependence of species aggregation patterns, whatever the spatial scale considered. However, we showed that species distribution patterns can be predicted, to an extent, at spatial scales much larger than previously investigated in this context. Such patterns may be explained by traits displaying phylogenetic conservatism (such as dispersal syndrome), but further studies are necessary to clearly identify them.},
-author = {R{\'{e}}jou-M{\'{e}}chain, Maxime and Flores, Olivier and Bourland, Nils and Doucet, Jean-Louis and F{\'{e}}t{\'{e}}k{\'{e}}, Richard F and Pasquier, Alexandra and Hardy, Olivier J},
-doi = {10.1111/j.1365-2745.2011.01873.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/R{\'{e}}jou-M{\'{e}}chain et al. - 2011 - Spatial aggregation of tropical trees at multiple spatial scales (suppl mater).doc:doc;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/R{\'{e}}jou-M{\'{e}}chain et al. - 2011 - Spatial aggregation of tropical trees at multiple spatial scales.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {1373--1381},
-title = {{Spatial aggregation of tropical trees at multiple spatial scales}},
-url = {http://dx.doi.org/10.1111/j.1365-2745.2011.01873.x},
-volume = {99},
-year = {2011}
-}
-@article{Naeem2003,
-abstract = {Experimental investigations of the relationship between biodiversity and ecosystem functioning (BEF) directly manipulate diversity then monitor ecosystem response to the manipulation. While these studies have generally confirmed the importance of biodiversity to the functioning of ecosystems, their broader significance has been difficult to interpret. The main reasons for this difficulty concern the small scales of the experiment, a bias towards plants and grasslands, and most importantly a general lack of clarity in terms of what attributes of functional diversity (FD) were actually manipulated. We review how functional traits, functional groups, and the relationship between functional and taxonomic diversity have been used in current BEF research. Several points emerged from our review. First, it is critical to distinguish between response and effect functional traits when quantifying or manipulating FD. Second, although it is widely done, using trophic position as a functional group designator does not fit the effect-response trait division needed in BEF research. Third, determining a general relationship between taxonomic and FD is neither necessary nor desirable in BEF research. Fourth, fundamental principles in community and biogeographical ecology that have been largely ignored in BEF research could serve to dramatically improve the scope and predictive capabilities of BEF research. We suggest that distinguishing between functional response traits and functional effect traits both in combinatorial manipulations of biodiversity and in descriptive studies of BEF could markedly improve the power of such studies. We construct a possible framework for predictive, broad-scale BEF research that requires integrating functional, community, biogeographical, and ecosystem ecology with taxonomy.},
-author = {Naeem, Shahid and Wright, Justin P.},
-doi = {10.1046/j.1461-0248.2003.00471.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Naeem, Wright - 2003 - Disentangling biodiversity effects on ecosystem functioning deriving solutions to a seemingly insurmountable prob.pdf:pdf},
-journal = {Ecology Letters},
-number = {6},
-pages = {567--579},
-title = {{Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00471.x/full},
-volume = {6},
-year = {2003}
-}
-@book{Bongers2001,
-abstract = {Nouragues is a tropical forest research station in French Guiana. It was established in 1986 for research on natural mechanisms of forest regeneration. Since then a lot of research has been done on this and related topics. This book provides an overview of the main research results, and focuses on plant communities, vertebrate communities and evolutionary ecology, frugivory and seed dispersal, and forest dynamics and recruitment. The appendices give (annoted) checklists of plants, birds, mammals, herpetofauna and fishes found in the same area.},
-doi = {10.1007/978-94-015-9821-7},
-editor = {Bongers, F. and Charles-Dominique, P. and Forget, P.-M. and Th{\'{e}}ry, M.},
-isbn = {978-1-4020-0123-9},
-publisher = {Springer Netherlands},
-title = {{Nouragues: dynamics and plant-animal interactions in a neotropical rainforest}},
-year = {2001}
-}
-@article{Rigby2002,
-abstract = {Plant‐level data from the Longitudinal Research Database of the US Bureau of the Census are employed to estimate the impact of agglomeration economies on industry productivity across US metropolitan areas. This analysis seeks to remedy three shortcomings of previous empirical studies of agglomeration economies: reliance on aggregate spatial or sectoral data; lack of attention to spatial dependence in data; and representation of agglomeration economies with vague proxies such as city‐size. We show how a number of establishment‐, industry‐, and city‐specific factors influence labor productivity across US cities, and we pay particular attention to separating the influence of different kinds of agglomeration economies on firm efficiency. Here we follow Marshall's Principles of Economics in examining the spatial concentration of input–output linkages, the character of local labor pools and embodied technological spillovers.},
-author = {Rigby, David L. and Essletzbichler, J{\"{u}}rgen},
-doi = {10.1093/jeg/2.4.407},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rigby, Essletzbichler - 2002 - Agglomeration economies and productivity differences in the US cities.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {'},
-pages = {407--432},
-title = {{Agglomeration economies and productivity differences in the US cities}},
-url = {https://academic.oup.com/joeg/article-abstract/2/4/407/932046/Agglomeration-economies-and-productivity},
-volume = {2},
-year = {2002}
-}
-@article{Bulmer1974,
-abstract = {An extension of MacArthur's "broken stick" model is proposed to explain why species abundances should be lognormally distributed. A method of fitting the compound Poisson lognormal distribution by maximum likelihood is described; a computer program is available for performing the calculations. It is shown how the information theory measure of species diversity can be estimated from the parameters of the fitted distribution.},
-author = {Bulmer, M. G.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bulmer - 1974 - On Fitting the Poisson Lognormal Distribution to Species-Abundance Data.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {101--110},
-title = {{On Fitting the Poisson Lognormal Distribution to Species-Abundance Data}},
-url = {http://www.jstor.org/stable/2529621},
-volume = {30},
-year = {1974}
-}
-@article{Pavoine2009,
-abstract = {Rao's quadratic entropy (QE) is a diversity index that includes the abundances of categories (e.g. alleles, species) and distances between them. Here we show that, once the distances between categories are fixed, QE can be maximized with a reduced number of categories and by several different distributions of relative abundances of the categories. It is shown that Rao's coefficient of distance (DISC), based on QE, can equal zero between two maximizing distributions, even if they have no categories in common. The consequences of these findings on the relevance of QE for understanding biological diversity are evaluated in three case studies. The behaviour of QE at its maximum is shown to be strongly dependent on the distance metric. We emphasize that the study of the maximization of a diversity index can bring clarity to what exactly is measured and enhance our understanding of biological diversity},
-annote = {Cited By (since 1996): 6
-Export Date: 1 January 2012
-Source: Scopus
-CODEN: TLPBA
-doi: 10.1016/j.tpb.2009.01.008
-PubMed ID: 19232526
-Language of Original Document: English
-Correspondence Address: Pavoine, S.; Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; email: sandrine.pavoine@zoo.ox.ac.uk},
-author = {Pavoine, Sandrine and Bonsall, Michael B.},
-doi = {10.1016/j.tpb.2009.01.008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Bonsall - 2009 - Biological diversity Distinct distributions can lead to the maximization of Rao's quadratic entropy.pdf:pdf},
-journal = {Theoretical Population Biology},
-number = {2-3},
-pages = {153--163},
-title = {{Biological diversity: Distinct distributions can lead to the maximization of Rao's quadratic entropy}},
-volume = {75},
-year = {2009}
-}
-@unpublished{Waagepetersen2017,
-abstract = {Kernel estimation is a popular approach to estimation of the pair correlation function function which is a fundamental spatial point process characteristic. Least squares cross validation was suggested by Guan (2007a) as a data-driven approach to select the kernel bandwidth. The method can, however, be computationally demanding for large point pattern data sets. We suggest a modified least squares cross validation approach that is asymptotically equivalent to the one proposed by Guan (2007a) but is computationally much faster.},
-author = {Waagepetersen, Rasmus and Jalilian, Abdollah},
-booktitle = {CSGB Research Reports},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Waagepetersen, Jalilian - 2017 - Fast bandwidth selection for estimation of the pair correlation function.pdf:pdf},
-number = {07},
-title = {{Fast bandwidth selection for estimation of the pair correlation function}},
-url = {http://math.au.dk/publs?publid=1106},
-year = {2017}
-}
-@article{Brulhart1998,
-abstract = {This article examines the location of manufacturing industries in the European Union. It draws on intra-industry trade measures for 1961–90 and on sectoral employment data by countries and regions. The analysis of employment data suggests that EU industry has become increasingly localized in the 1980s. Increasing-returns industries are strongly concentrated at the economic core of the EU and display low levels of intra-industry trade. High-tech industries are also strongly localized, but show no centre-periphery gradient and no specific pattern of intra-industry trade. The main potential for future specialization appears to remain in sectors sensitive to labour costs, which are still relatively dispersed and have high levels of intra-industry trade. Employment in these industries is shifting towards the EU periphery. ‘Neoclassical' determinants of international specialization are thus likely to dominate the ongoing adjustment process in EU manufacturing.},
-author = {Br{\"{u}}lhart, Marius},
-doi = {10.1111/1468-5965.00113},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Journal of Common Market Studies},
-number = {3},
-pages = {319--346},
-title = {{Trading Places: Industrial Specialisation in the European Union}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1468-5965.00113/abstract},
-volume = {36},
-year = {1998}
-}
-@book{Eisemberg2017,
-author = {Eisemberg, Carla Camilo and Reynolds, Stephen J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eisemberg, Reynolds - 2017 - An Introduction to Wildlife Conservation in the Brazilian Amazon A View from Northern Australia.pdf:pdf},
-isbn = {9780646973227},
-title = {{An Introduction to Wildlife Conservation in the Brazilian Amazon: A View from Northern Australia}},
-year = {2017}
-}
-@book{Dagnelie1973,
-author = {Dagnelie, Pierre},
-edition = {2{\`{e}}me ed.},
-publisher = {Les presses agronomiques de Gembloux},
-title = {{Th{\'{e}}orie et m{\'{e}}thodes statisiques}},
-volume = {1},
-year = {1973}
-}
-@article{Faith2013,
-abstract = {Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying feature diversity measures possible future uses and benefits or option values. Interpretation of PD as counting-up features is the basis for an emerging broad family of PD calculations, of use to both biodiversity researchers and decision makers. Many of these calculations extend conventional species-level indices to the features level. Useful PD calculations include PD complementarity and endemism, Hill and Valley numbers incorporating abundance, and PD dissimilarities. A flexible analysis framework is provided by expected PD calculations, applied to either probabilities of extinction or presence-absence. Practical extensions include phylogenetic risk analysis and measures of distinctiveness and endemism. These support the integration of phylogenetic diversity into biodiversity conservation and monitoring programs.},
-author = {Faith, Daniel P.},
-doi = {10.1111/nyas.12186},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faith - 2013 - Biodiversity and evolutionary history Useful extensions of the PD phylogenetic diversity assessment framework.pdf:pdf},
-journal = {Annals of the New York Academy of Sciences},
-pages = {69--89},
-title = {{Biodiversity and evolutionary history: Useful extensions of the PD phylogenetic diversity assessment framework}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/nyas.12186/full},
-volume = {1289},
-year = {2013}
-}
-@article{Post2000,
-abstract = {Food-chain length is an important characteristic of ecological communities: it influences community structure, ecosystem functions and contaminant concentrations in top predators. Since Elton first noted that food-chain length was variable among natural systems, ecologists have considered many explanatory hypotheses, but few are supported by empirical evidence. Here we test three hypotheses that predict food-chain length to be determined by productivity alone (productivity hypothesis), ecosystem size alone (ecosystem-size hypothesis) or a combination of productivity and ecosystem size (productive-space hypothesis). The productivity and productive-space hypotheses propose that food-chain length should increase with increasing resource availability; however, the productivity hypothesis does not include ecosystem size as a determinant of resource availability. The ecosystem-size hypothesis is based on the relationship between ecosystem size and species diversity, habitat availability and habitat heterogeneity. We find that food-chain length increases with ecosystem size, but that the length of the food chain is not related to productivity. Our results support the hypothesis that ecosystem size, and not resource availability, determines food-chain length in these natural ecosystems.},
-author = {Post, David M. and Pace, Michael L. and Hairston, Nelson J.},
-doi = {10.1038/35016565},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Post, Pace, Hairston - 2000 - Ecosystem size determines food-chain length in lakes.pdf:pdf},
-journal = {Nature},
-number = {6790},
-pages = {1047--1049},
-title = {{Ecosystem size determines food-chain length in lakes.}},
-volume = {405},
-year = {2000}
-}
-@article{Terborgh1999,
-abstract = {Primary tropical forests comprise a mosaic of mature, gap and build- ing phase patches, resulting in great spatial variation in the distribution of foliage. Light may consequently penetrate into the forest interior over a wide range of angles. It thus seems possible that understorey tree species might be adapted for distinct understorey light conditions. At the Cocha Cashu Biological Station in Madre de Dios, Peru, there are two understorey treelets distinguished by con- trasting crown architectures. One, Neea chlorantha (Nyctaginaceae), possesses a much-branched superstructure and displays a smoothly contoured shell of drooping elliptical leaves. The other, Rinorea viridifolia (Violaceae), displays planar arrays of horizontally-oriented obovate leaves held on whorls of stiffly radiating horizontal branches. With the aid of hemispherical photography and the program CANOPY, the light environment at large within a 2.25-ha permanent tree plot, and above and below the crowns of Neea and Rinorea treelets, was investigated. Available light (measured as uncorrected indirect site factor (ISFU) in CANOPY) at control points showed a log-linear increase with height from 2.1 to 14.2 m. The relative amount of lateral illumination also increased with height. Photographs were taken just above and below the crowns of 50 Neea and 50 Rinorea treelets. Neea crowns were more effect- ive at intercepting light from overhead sources, whereas Rinorea crowns were more effective at intercepting light from lateral sources. Adult Neea and Rinorea treelets occurred at locations in the forest where they were exposed to differing angular distributions of incident light, suggesting that the two species were engaged in a form of resource partitioning, a conclusion that is in conflict with the non- equilibrium model of tropical forest tree species diversity. It is suggested that tropical tree species diversity is, at least in part, a product of adaptive specializa- tion to a spatially heterogeneous light environment.},
-author = {Terborgh, John and Mathews, Jeffrey},
-doi = {10.1017/S0266467499001157},
-isbn = {02664674},
-issn = {02664674},
-journal = {Journal of Tropical Ecology},
-number = {6},
-pages = {S0266467499001157},
-title = {{Partitioning of the understorey light environment by two Amazonian treelets}},
-url = {http://www.journals.cambridge.org/abstract{\_}S0266467499001157},
-volume = {15},
-year = {1999}
-}
-@article{Thompson1999a,
-abstract = {Coevolution is one of the major processes organizing the earth's biodiversity. The need to understand coevolution as an ongoing process has grown as ecological concerns have risen over the dynamics of rapidly changing biological communities, the con- servation of genetic diversity, and the population biology of diseases. The biggest current challenge is to understand how coevolution op- erates across broad geographic landscapes, linking local ecological processes with phylogeographic patterns. The geographic mosaic the- ory of coevolution provides a framework for asking how coevolution continually reshapes interactions across different spatial and temporal scales. It produces specific hypotheses on how geographically struc- tured coevolution differs from coevolution at the local scale. It also provides a framework for understanding how local maladaptation can result from coevolution and why coevolved interactions may rarely produce long lists of coevolved traits that become fixed within species. Long-term field studies of the same interaction across mul- tiple communities and spatially structured mathematical models are together beginning to show that coevolution may be a more im- portant ongoing process than had been indicated by earlier empirical and theoretical studies lacking a geographic perspective.},
-author = {Thompson, John N.},
-doi = {10.1086/303208},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Thompson - 1999 - Specific Hypotheses on the Geographic Mosaic of Coevolution.pdf:pdf},
-journal = {The American Naturalist},
-number = {S5},
-pages = {S1--S14},
-title = {{Specific Hypotheses on the Geographic Mosaic of Coevolution}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/303208},
-volume = {153},
-year = {1999}
-}
-@article{Chao1992,
-abstract = {Assume that a random sample is drawn from a population with unknown number of classes and possibly unequal class probabilities. A nonparametric estimation technique is proposed to estimate the number of classes using the idea of sample coverage, which is defined as the sum of the cell probabilities of the observed classes. Since expected sample coverage can be well estimated, we were motivated to find its role in the estimation of the number of classes. This work generalizes the result of Esty to a nonparametric approach and extends Darroch and Ratcliff to incorporate the heterogeneity of the class probabilities. The coefficient of variation of the class sizes is shown to play an important role in the recommended estimation procedures. The performance of the proposed estimators is investigated by means of Monte Carlo simulations.},
-author = {Chao, Anne and Lee, Shen-Ming},
-doi = {10.1080/01621459.1992.10475194},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Lee - 1992 - Estimating the Number of Classes Via Sample Coverage.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {417},
-pages = {210--217},
-title = {{Estimating the Number of Classes Via Sample Coverage}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1992.10475194},
-volume = {87},
-year = {1992}
-}
-@article{Pascal1995,
-abstract = {Les diff{\'{e}}rents niveaux de complexit{\'{e}} de la for{\^{e}}t dense humide tropicale posent {\`{a}} l'analyste des donn{\'{e}}es et au mod{\'{e}}lisateur plusieurs types de probl{\`{e}}mes. Dans un premier temps sont donn{\'{e}}s quelques exemples de la difficult{\'{e}} {\`{a}} r{\'{e}}aliser des {\'{e}}chantillonnages appropri{\'{e}}s aux hypoth{\`{e}}ses {\`{a}} tester, par suite de l'h{\'{e}}t{\'{e}}rog{\'{e}}n{\'{e}}it{\'{e}} de la formation. L'h{\'{e}}t{\'{e}}rog{\'{e}}n{\'{e}}it{\'{e}}, aussi bien structurale que floristique, peut r{\'{e}}sulter des variations de topographie, de nature et de propri{\'{e}}t{\'{e}}s du sol, des conditions de drainage, de l'exposition, etc., mais aussi de l'histoire de la for{\^{e}}t. Elle peut appara{\^{i}}tre {\`{a}} diff{\'{e}}rentes {\'{e}}chelles spatiales qu'il n'est pas toujours facile de mettre en {\'{e}}vidence. Les probl{\`{e}}mes d'{\'{e}}chelle spatiale et de temps, li{\'{e}}s {\`{a}} la dynamique de fonctionnement des for{\^{e}}ts denses humides tropicales, sont abord{\'{e}}s dans la seconde partie. Sous le m{\^{e}}me terme de chablis sont group{\'{e}}s, en r{\'{e}}alit{\'{e}}, des ph{\'{e}}nom{\`{e}}nes vari{\'{e}}s mettant en jeu des m{\'{e}}canismes de fermeture diff{\'{e}}rents. Depuis l'{\'{e}}volution simple d'une {\'{e}}co-unit{\'{e}}, {\`{a}} partir d'un chablis {\'{e}}l{\'{e}}mentaire, jusqu'aux grandes ouvertures produites par des chablis multiples et r{\'{e}}currents, tous les interm{\'{e}}diaires se rencontrent, cr{\'{e}}ant dans la formation des zones {\'{e}}voluant {\`{a}} des vitesses et selon des processus diff{\'{e}}rents. D'autres m{\'{e}}canismes sont {\'{e}}galement {\`{a}} l'oeuvre dans la dynamique foresti{\`{e}}re. Le plus {\'{e}}vident est la substitution d'un arbre par un autre ayant pouss{\'{e}} dans son voisinage imm{\'{e}}diat, sans qu'il y ait de chablis v{\'{e}}ritable. Ce processus implique la mort sur pied de l'arbre {\^{a}}g{\'{e}}. Un autre m{\'{e}}canisme, plus complexe, appara{\^{i}}t lorsque la fr{\'{e}}quence des chablis est faible et que les arbres ont une dur{\'{e}}e de vie importante : la formation s'organise alors en unit{\'{e}}s fonctionnelles circulaires glissant progressivement les unes par rapport aux autres. Un troisi{\`{e}}me type de probl{\`{e}}me se pose pour l'{\'{e}}tude des structures des populations. Les esp{\`{e}}ces ont, en majorit{\'{e}}, des effectifs trop r{\'{e}}duits (sans parler des esp{\`{e}}ces rares) pour que leurs populations puissent {\^{e}}tre correctement {\'{e}}tudi{\'{e}}es. Peu d'esp{\`{e}}ces sont suffisamment bien repr{\'{e}}sent{\'{e}}es pour cela. L'inconv{\'{e}}nient est faible pour la r{\'{e}}alisation de mod{\`{e}}les globaux, de production par exemple, mais tr{\`{e}}s important pour les {\'{e}}tudes centr{\'{e}}es sur la biodiversit{\'{e}}. Enfin, l'analyse des accroissements montre qu'il est le plus souvent impossible d'attribuer {\`{a}} une esp{\`{e}}ce donn{\'{e}}e une courbe de croissance type en fonction du temps : tous les cas de figures se rencontrent pour une m{\^{e}}me esp{\`{e}}ce, ce qui constitue un obstacle important {\`{a}} la mod{\'{e}}lisation.},
-author = {Pascal, Jean-pierre},
-issn = {0249-7395},
-journal = {Revue d'{\'{e}}cologie},
-pages = {237--249},
-title = {{Quelques exemples de probl{\`{e}}mes pos{\'{e}}s {\`{a}} l'analyste et au mod{\'{e}}lisateur par la complexit{\'{e}} de la for{\^{e}}t tropicale humide}},
-url = {http://hdl.handle.net/2042/54806},
-volume = {50},
-year = {1995}
-}
-@book{Bellman1970,
-address = {New York},
-author = {Bellman, R. and Cooke, K. L. and Lockett, J. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bellman, Cooke, Lockett - 1970 - Algorithms, Graphs and Computers.pdf:pdf},
-publisher = {Academic Press, Inc.},
-title = {{Algorithms, Graphs and Computers}},
-year = {1970}
-}
-@article{Wiegand2016,
-abstract = {Model testing is a central step of spatial point pattern analysis, which allows ecologists to judge if their data agree with ecological hypotheses. We present a simple and elegant solution of a challenging problem: the construction of a goodness-of-fit envelope test with prescribed significance level $\alpha$. Our new Analytical Global Envelope (AGE) test is not restricted to the narrow frame of complete spatial randomness testing and its envelopes can be determined by mathematical calculations. This allows us to investigate the influence of key settings of the AGE test on the width of the envelope strip. To circumvent some assumptions of the simulation-free AGE test we present a corresponding Simulation-Based Global Envelope (SBGE) test. The envelope strip of the AGE and the SBGE test encircles the range of a summary function such as the pair correlation function under the null model, and it has the desired property that the null hypothesis can be rejected with significance level $\alpha$ if the empirical summary function wanders outside the envelopes. The AGE test can be applied under the mild conditions that the values of the summary functions under the null model are (approximately) normally distributed and are (approximately) independent for different distance bins rj. The SBGE test requires only the independence assumption. The width of the strip of the AGE envelopes scales for a broad range of point processes with 1/n, where n is the number of points. This casts doubt about attempts of goodness-of-fit testing with low n (say {\textless}100). The AGE and SBGE test operate with wider envelope strips than the classical “pointwise” test. Therefore, the pointwise test has to be considered as too liberal. Furthermore, we show that the width of the AGE/SBGE strip increases approximately with ln(b), where b is the number of distance bins. For example, the AGE/SBGE envelopes are for b = 20 more than 50{\%} wider than the corresponding pointwise envelopes. Our study opens up new avenues to the test problem in point pattern statistics and the new AGE and SBGE tests can be widely applied in ecology to improve the practice in null model testing.},
-author = {Wiegand, Thorsten and Grabarnik, Pavel and Stoyan, Dietrich},
-doi = {10.1002/ecs2.1365},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand, Grabarnik, Stoyan - 2016 - Envelope tests for spatial point patterns with and without simulation.pdf:pdf},
-journal = {Ecosphere},
-pages = {1--18},
-title = {{Envelope tests for spatial point patterns with and without simulation}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1365/abstract},
-volume = {7},
-year = {2016}
-}
-@article{Hart1971,
-abstract = {In recent years, economists have begun to use the entropy, or redundancy, of a size distribution to measure the extent to which business is concentrated in the control of giant firms. This paper compares these new measures derived from information theory with the classical statistical measures of dispersion and with traditional measures of business concentration derived from the cumulative concentration curve. It shows that when the number of firms is large enough to use statistical distribution theory, the classical statistical measures are superior to the entropy or the redundancy. When the number of firms is small, the entropy is superior to the redundancy, but both are inferior to the traditional measures of concentration derived from the cumulative concentration curve. Consequently, there is little point in using the information theory measures to measure business concentration.},
-author = {Hart, P. E.},
-doi = {10.2307/2343975},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hart - 1971 - Entropy and Other Measures of Concentration.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
-number = {1},
-pages = {73--85},
-title = {{Entropy and Other Measures of Concentration}},
-url = {http://www.jstor.org/stable/2343975},
-volume = {134},
-year = {1971}
-}
-@incollection{Glaeser2004,
-address = {Amsterdam},
-author = {Glaeser, Edward L. and Kahn, Matthew E.},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Glaeser, Kahn - 2004 - Sprawl and Urban Growth.pdf:pdf},
-keywords = {Glaeser (2003).pdf},
-mendeley-tags = {Glaeser (2003).pdf},
-pages = {73 p.},
-publisher = {Elsevier. North Holland},
-title = {{Sprawl and Urban Growth}},
-year = {2004}
-}
-@article{VanValen1976,
-abstract = {Oaks exemplify problems wirh the reproductive species concept which motivate a reconsideration of the use and nature of species. Ecology is important in the reconsider- ation. The species level is usually overemphasized in evolutionary thought; selection acts on phenotypes and any mutualistic units. Standard definitions tend to inhibit free conceptual progress. Multispecies, sets of broadly sympatric species that exchange genes, may occur among animals as well as plants and may conceivably bridge kingdoms. This phenomenon can be adaptively important. There may be taxa without species. The degree of modality of adaptive zones can be investigated empirically.},
-author = {{Van Valen}, Leigh},
-doi = {10.2307/1219444},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Van Valen - 1976 - Ecological species, multispecies, and oaks.pdf:pdf},
-journal = {Taxon},
-number = {2/3},
-pages = {233--239},
-title = {{Ecological Species, Multispecies, and Oaks}},
-url = {http://www.jstor.org/stable/1219444},
-volume = {25},
-year = {1976}
-}
-@article{Garnier2001a,
-abstract = {Specific leaf area (leaf area to dry mass ratio), leaf dry matter content (leaf dry mass to saturated fresh mass ratio) and leaf nitrogen concentration (LNC) have been proposed as indicators of plant resource use in data bases of plant functional traits. We tested whether species ranking based on these traits was repeatable by studying spatio-temporal variations in specific leaf area and leaf dry matter content of water-saturated leaves (SLASAT and LDMCSAT), as well as in LNC, for 57 herbaceous and woody species (or subsets thereof) growing under the Mediterranean climate of southern France. Interseason and intersite variations were more pronounced than interannual variations, but species ranking for a given trait remained mostly consistent in space and time. Classifications based on LDMCSAT were generally more repeatable across years and sites, whereas those based on SLASAT were more stable over seasons. LNC usually gave the least repeatable classifications. Species rankings were not completely similar for the three traits. Discussion of reproducibility, ease of trait measurement, as well as trait–function relationships led us to propose that measurements of the leaf traits, SLASAT and/or LDMCSAT, were the most suitable in large screening programmes.},
-author = {Garnier, Eric and Laurent, G{\'{e}}rard and Bellmann, Astrid and Debain, S. and Berthelier, P. and Ducout, B. and Roumet, Catherine and Navas, Marie-Laure},
-doi = {10.1046/j.0028-646x.2001.00239.x},
-file = {::},
-journal = {New Phytologist},
-number = {1},
-pages = {69--83},
-title = {{Consistency of species ranking based on functional leaf traits}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.0028-646x.2001.00239.x/abstract},
-volume = {152},
-year = {2001}
-}
-@article{Rathbun1994,
-abstract = {A marked spatial point pattern of trees and their diameters is the result of a dynamic biological process that takes place over time as well as space. Such patterns can be modeled as realizations of marked space-time survival point processes, where trees are born at some random location and time and then live, grow, and produce offspring in a random fashion. A model for a marked space-time survival point process is fit to data from a longleaf pine (Pinus palustris) forest in southern Georgia. The space-time survival point process is divided into three components: a birth process, a growth process, and a survival process. Each of the component processes is analyzed individually, from which conclusions regarding the dynamic ecological processes can be made. By using this reductionist approach, questions concerning each individual process can be addressed that might not have been answerable otherwise.},
-author = {Rathbun, Stephen L. and Cressie, Noel A.},
-doi = {10.2307/2290979},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rathbun, Cressie - 1994 - A Space-Time Survival Point Process for a Longleaf Pine Forest in Southern Georgia.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {428},
-pages = {1164--1174},
-title = {{A Space-Time Survival Point Process for a Longleaf Pine Forest in Southern Georgia}},
-url = {https://www.jstor.org/stable/2290979},
-volume = {89},
-year = {1994}
-}
-@article{Lasinio2017,
-abstract = {The analysis of benthic assemblages is a valuable tool to describe the ecological status of transitional water ecosystems, but species are extremely sensitive and respond to both microhabitat and seasonal differences. The identification of changes in the composition of the macrobenthic community in specific microhabitats can then be used as an “early warning” for environmental changes which may affect the economic and ecological importance of lagoons, through their provision of Ecosystem Services. From a conservational point of view, the appropriate definition of the spatial aggregation level of microhabitats or local communities is of crucial importance. The main objective of this work is to assess the role of the spatial scale in the analysis of lagoon biodiversity. First, we analyze the variation in the sample coverage for alternative aggregations of the monitoring stations in three lagoons of the Po River Delta. Then, we analyze the variation of a class of entropy indices by mixed effects models, properly accounting for the fixed effects of biotic and abiotic factors and random effects ruled by nested sources of variability corresponding to alternative definitions of local communities. Finally, we address biodiversity partitioning by a generalized diversity measure, namely the Tsallis entropy, and for alternative definitions of the local communities. The main results obtained by the proposed statistical protocol are presented, discussed and framed in the ecological context.},
-author = {Lasinio, Giovanna Jona and Pollice, Alessio and Marcon, Eric and Fano, Elisa Anna},
-doi = {10.1016/j.ecolind.2017.05.037},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lasinio et al. - 2017 - Assessing the role of the spatial scale in the analysis of lagoon biodiversity . A case-study on the macrobenthi.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {303--315},
-title = {{Assessing the role of the spatial scale in the analysis of lagoon biodiversity . A case-study on the macrobenthic fauna of the Po River Delta}},
-url = {http://dx.doi.org/10.1016/j.ecolind.2017.05.037},
-volume = {80},
-year = {2017}
-}
-@article{Loreau2004,
-abstract = {Functional redundancy has often been assumed as an intuitive null hypothesis in biodiversity experiments, but theory based on the classical Lotka-Volterra competition model shows that functional redundancy sensu stricto is incompatible with stable coexistence. Stable coexistence requires differences between species which lead to functional complementarity and differences between the yields of mixtures and monocultures. Only a weaker version of functional redundancy, i.e. that mixture yields lie within the range of variation of monoculture yields, is compatible with stable coexistence in Lotka-Volterra systems. Spatial and temporal environmental variability may provide room for functional redundancy at small spatial and temporal scales, but is not expected to do so at the larger scales at which environmental variations help maintain coexistence. Neutral coexistence of equivalent competitors, non-linear per capita growth rates, and lack of correlation between functional impact and biomass may provide the basis for the existence of functional redundancy in natural ecosystems. Overall, there is a striking parallel between the conditions that allow stable coexistence and those that allow overyielding.},
-author = {Loreau, Michel},
-doi = {10.1111/j.0030-1299.2004.12685.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loreau - 2004 - Does functional redundancy exist.pdf:pdf},
-journal = {Oikos},
-number = {3},
-pages = {606--611},
-title = {{Does functional redundancy exist?}},
-url = {onlinelibrary.wiley.com/doi/10.1111/j.0030-1299.2004.12685.x/abstract},
-volume = {104},
-year = {2004}
-}
-@article{Bacaro2007,
-abstract = {Question: The utility of beta ($\beta$-) diversity measures that incorporate information about the degree of taxonomic (dis) similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of $\beta$-diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot-to-plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher-level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify $\beta$-diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic $\beta$-diversity incorporates not only species richness, but also information about the degree of higher-order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of $\beta$-diversity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80{\%} of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher-order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot-to-plot similarity is only needed if we are interested in the residual system's variation that is related to the higher-order taxonomic structure of a pair of species plots. {\textcopyright} IAVS; Opulus Press.},
-annote = {Cited By (since 1996):13
-Export Date: 12 March 2014
-Source: Scopus
-CODEN: JVESE
-Language of Original Document: English
-Correspondence Address: Bacaro, G.; Department of Environmental Science, University of Siena, Via P.A. Mattioli 4, 53100 Siena, Italy; email: bacaro@unisi.it},
-author = {Bacaro, Giovanni and Ricotta, Carlo and Mazzoleni, S.},
-doi = {10.1111/j.1654-1103.2007.tb02595.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bacaro, Ricotta, Mazzoleni - 2007 - Measuring beta-diversity from taxonomic similarity.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {6},
-pages = {793--798},
-title = {{Measuring beta-diversity from taxonomic similarity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2007.tb02595.x/abstract},
-volume = {18},
-year = {2007}
-}
-@book{Brillouin1962,
-abstract = {The 2nd edition adds material on the role of errors in scientific observation and a critical discussion of determinism from the standpoint of information theory to the material of the 1st edition, which applied information theory to a great number of problems of physics, including: the analysis of signals; thermodynamics; Brownian movement; thermal agitation in electronic tubes, rectifiers, etc.; entropy; Maxwell's demon; Szilard's well-informed heat engine; observations and error; communication; and computing. The new material on determinism leads to Brillouin's "matter of fact" point of view that strict determinism is impossible in scientific prediction because the high cost at some point makes increasing accuracy unattainable. The limit of accuracy is a practical rather than an inevitable limitation in the logical sense. The limitations can be formulated in precise ways by quantum conditions and information theory and should be included in the physical theory.},
-address = {Oxford},
-author = {Brillouin, L{\'{e}}on},
-chapter = {351},
-edition = {2nd ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brillouin - 1962 - Science and information theory.pdf:pdf},
-isbn = {9780486497556},
-publisher = {Academic Press},
-title = {{Science and information theory}},
-url = {http://store.doverpublications.com/0486497550.html},
-year = {1962}
-}
-@article{Janzen1970,
-abstract = {A high number of tree species, low density of adults of each species, and long distances between conspecific adults are characteristic of many low-land tropical forest habitats. I propose that these three traits, in large part, are the result of the action of predators on seeds and seedlings. A model is presented that allows detailed examination of the effect of different predators, dispersal agents, seed-crop sizes, etc. on these three traits. In short, any event that increases the efficiency of the predators at eating seeds and seedlings of a given tree species may lead to a reduction in population density of the adults of that species and/or to increased distance between new adults and their parents. Either event will lead to more space in the habitat for other species of trees, and therefore higher total number of tree species, provided seed sources are available over evolutionary time. As one moves from the wet lowland tropics to the dry tropics or temperate zones, the seed and seedling predators in a habitat are hypothesized to be progressively less efficient at keeping one or a few tree species from monopolizing the habitat through competitive superiority. This lowered efficiency of the predators is brought about by the increased severity and unpredictability of the physical environment, which in turn leads to regular or erratic escape of large seed or seedling cohorts from the predators.},
-author = {Janzen, Daniel H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Janzen - 1970 - Herbivores and the number of species in tropical forests.pdf:pdf},
-journal = {The American Naturalist},
-number = {940},
-pages = {501--528},
-title = {{Herbivores and the number of species in tropical forests}},
-url = {http://www.jstor.org/stable/2459010},
-volume = {104},
-year = {1970}
-}
-@book{Halle1978,
-author = {Hall{\'{e}}, Francis and Oldeman, Roelof A. A. and Tomlinson, Philip B.},
-isbn = {3-540-08494-0},
-publisher = {Springer-Verlag},
-title = {{Tropical Trees and Forests: an Architectural Analysis}},
-url = {http://www.springer.com/la/book/9783642811920},
-year = {1978}
-}
-@article{Figueiredo2002,
-abstract = {An investor's home bias in industrial location decisions may stem from personal factors, social capital, other non-transferable assets, and imperfect information about the urban and regional environment. This paper explores the distinction between home-base and non-home location decisions in Portugal. We reach two important conclusions. First, the introduction of a variable accounting for prior base of economic activity significantly improves the statistical results. Second, we find that the weighting of distinct location attributes differs between home and non-home locations. Notably, non-home location choices are strongly governed by agglomeration economies and proximity to major urban centers, possibly replicating prior location decisions to economize on search costs. The results also enable us to quantify the investor's willingness to opt for a possible home-field advantage; for example, entrepreneurs accept over three times higher labor costs to compete in their resident area of business.},
-author = {Figueiredo, Oct{\'{a}}vio and Guimar{\~{a}}es, Paulo and Woodward, Douglas P.},
-doi = {10.1016/S0094-1190(02)00006-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Figueiredo, Guimar{\~{a}}es, Woodward - 2002 - Home-field advantage location decisions of Portuguese entrepreneurs.pdf:pdf},
-journal = {Journal of Urban Economics},
-pages = {341--361},
-title = {{Home-field advantage: location decisions of Portuguese entrepreneurs}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119002000062},
-volume = {52},
-year = {2002}
-}
-@article{Guan2011,
-abstract = {We introduce novel regression extrapolation based methods to correct the often large bias in subsampling variance estimation as well as hypothesis testing for spatial point and marked point processes. For variance estimation, our proposed estimators are linear combinations of the usual subsampling variance estimator based on subblock sizes in a continuous interval. We show that they can achieve better rates in mean squared error than the usual subsampling variance estimator. In particular, for n×n observation windows, the optimal rate ofn-2can be achieved if the data have a finite dependence range. For hypothesis testing, we apply the proposed regression extrapolation directly to the test statistics based on different subblock sizes, and therefore avoid the need to conduct bias correction for each element in the covariance matrix used to set up the test statistics. We assess the numerical performance of the proposed methods through simulation, and apply them to analyze a tropical forest data set. {\textcopyright} 2010, The International Biometric Society.},
-annote = {Export Date: 22 January 2012
-Source: Scopus
-CODEN: BIOMA
-Language of Original Document: English
-Correspondence Address: Guan, Y.; Division of Biostatistics, Yale University, email., New Haven, CT 06520, United States; email: yongtao.guan@yale.edu},
-author = {Guan, Yongtao},
-doi = {10.1111/j.1541-0420.2010.01517.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guan - 2011 - Bias-Corrected Variance Estimation and Hypothesis Testing for Spatial Point and Marked Point Processes Using Subsampling.pdf:pdf},
-journal = {Biometrics},
-number = {3},
-pages = {926--936},
-title = {{Bias-Corrected Variance Estimation and Hypothesis Testing for Spatial Point and Marked Point Processes Using Subsampling}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-80052814276{\&}partnerID=40{\&}md5=d4d671f5b9635cc24900c1706635b815},
-volume = {67},
-year = {2011}
-}
-@incollection{Steel1953,
-author = {Steel, G. D.},
-booktitle = {Biometrics Unit Technical Reports},
-chapter = {BU-39-M},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Steel - 1953 - Relation Between Poisson and Multinomial Distributions.pdf:pdf},
-pages = {1--2},
-publisher = {Cornell University. Biometrics Unit.},
-title = {{Relation Between Poisson and Multinomial Distributions}},
-url = {http://hdl.handle.net/1813/32480},
-year = {1953}
-}
-@phdthesis{Paget1999,
-author = {Paget, Dominique},
-booktitle = {Sp{\'{e}}cialit{\'{e}} sciences foresti{\`{e}}res},
-publisher = {ENGREF},
-title = {{Etude de la diversit{\'{e}} spatiale des {\'{e}}cosyst{\`{e}}mes forestiers guyanais : r{\'{e}}flexion m{\'{e}}thodologique et application}},
-year = {1999}
-}
-@article{Lang2014,
-abstract = {For a decade, distance-based methods have been widely employed and constantly improved in the field of spatial economics. These methods are a very useful tool for accurately evaluating the spatial distribution of plants or retail stores, for example (Duranton and Overman, 2008). In this paper, we introduce a new distance-based statistical measure for evaluating the spatial concentration of economic activities. To our knowledge, the m function is the first relative density function to be proposed in the economics literature. This tool supplements the typology of distance-based methods recently drawn up by Marcon and Puech (2012). By considering several theoretical and empirical examples, we show the advantages and the limits of the m function for detecting spatial structures in economics. JEL},
-author = {Lang, Gabriel and Marcon, Eric and Puech, Florence},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lang, Marcon, Puech - 2015 - Distance-Based Measures of Spatial Concentration Introducing a Relative Density Function.pdf:pdf},
-journal = {HAL},
-number = {version 3},
-title = {{Distance-Based Measures of Spatial Concentration: Introducing a Relative Density Function}},
-url = {https://hal.archives-ouvertes.fr/hal-01082178},
-volume = {01082178},
-year = {2015}
-}
-@article{Nee2006,
-author = {Nee, Sean and Colegrave, Nick and West, Stuart A. and Grafen, Alan},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nee et al. - 2006 - Response to comment on The illusion of invariant quantities in life histories.pdf:pdf},
-journal = {Science},
-number = {5771},
-pages = {U3--U3},
-title = {{Response to comment on "The illusion of invariant quantities in life histories"}},
-volume = {312},
-year = {2006}
-}
-@article{Ekschmitt1998,
-abstract = {This paper evaluates theoretical arguments and empirical evidence on the interrelation of soil biodiversity and ecological functioning, in order to identify appropriate methodologies and promising fields of investigation. Predictions from a range of general theories are evaluated against the background of empirical findings and results from models on specific soil ecosystems with reference to the functional effects of species losses (1) within trophic levels, (2) in food-webs, and (3) those that depend on the size of the spatial scale. Difficulties in proving species richness effects empirically arise because (i) a range of mechanisms can compensate species richness effects, (ii) predictions on the effects of species richness are context-dependent, which renders valid generalisations less likely, and (iii) species richness effects are of a probabilistic, rather than a deterministic nature. Generally, the effects of changes in species richness are likely to be stronger in species-poor communities than in species-rich communities. The authors deduce the hypotheses that (a) the species richness within trophic levels is likely to reduce functional gaps in space and time, (b) the species richness across trophic levels of the decomposer food web can enhance synchronisation of subprocesses of nutrient cycling, and (c) differences in species richness are likely to be more pronounced on larger spatial scales. The authors infer that an explicit consideration of spatiotemporal variation is essential in experimentation, as well as in modelling, in order to analyse species richness-function relationships. (C) 1998 Elsevier Science B.V.},
-author = {Ekschmitt, K. and Griffiths, B. S.},
-doi = {10.1016/S0929-1393(98)00119-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ekschmitt, Griffiths - 1998 - Soil biodiversity and its implications for ecosystem functioning in a heterogeneous and variable environme.pdf:pdf},
-journal = {Applied Soil Ecology},
-number = {3},
-pages = {201--215},
-title = {{Soil biodiversity and its implications for ecosystem functioning in a heterogeneous and variable environment}},
-url = {http://www.sciencedirect.com/science/article/pii/S092913939800119X},
-volume = {10},
-year = {1998}
-}
-@article{Gower1966,
-abstract = {This paper is concerned with the representation of a multivariate sample of size n as points P1, P2, ..., PI in a Euclidean space. The interpretation of the distance A(Pi, Pj) between the ith andjth members of the sample is discussed for some commonly used types of analysis, including both Q and R techniques. When all the distances between n points are known a method is derived which finds their co-ordinates referred to principal axes. A set of necessary and sufficient conditions for a solution to exist in real Euclidean space is found. Q and R techniques are defined as being dual to one another when they both lead to a set of n points with the same inter-point distances. Pairs of dual techniques are derived. In factor analysis the distances between points whose co-ordinates are the estimated factor scores can be interpreted as D2 with a singular dispersion matrix},
-author = {Gower, J. C.},
-doi = {10.1093/biomet/53.3-4.325},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gower - 1966 - Some distance properties of latent root and vector methods used in multivariate analysis.pdf:pdf},
-journal = {Biometrika},
-number = {3},
-pages = {325--338},
-title = {{Some distance properties of latent root and vector methods used in multivariate analysis}},
-url = {http://biomet.oxfordjournals.org/content/53/3-4/325.short},
-volume = {53},
-year = {1966}
-}
-@article{Wright1943,
-author = {Wright, Sewall},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright - 1943 - Isolation by Distance.pdf:pdf},
-journal = {Genetics},
-pages = {114--138},
-title = {{Isolation by Distance}},
-volume = {28},
-year = {1943}
-}
-@article{Louf2015a,
-abstract = {The spatial distribution of income shapes the structure and organisation of cities and its understanding has broad societal implications. Despite an abundant literature, many issues remain however unclear: there is no clear definition of what segregation is, no unambiguous definition of income classes, no clear way to identify neighborhoods, and no method to deal with the polycentric organization of large cities. In this paper, we address all these questions within a unique theoretical framework. We assume that households belonging to the same class tend to live close to each other, and households from different classes tend to avoid one another. Applied to the US 2000 Census Income data, 3 distinct classes emerge from the clustering of the original 16 income classes. Using these unambiguously defined classes, we cluster together contiguous similar areas and find that the number of clusters for each category scales with the city population, an effect that is more pronounced for rich households. Finally, using the density -- and not the distance to a center which is meaningless in polycentric cities -- we find that the richer class is overrepresented in high density zones, especially for larger cities. This suggests that density is a relevant factor for understanding the income structure of cities and might explain some of the differences observed between US and European cities.},
-archivePrefix = {arXiv},
-arxivId = {1511.04268},
-author = {Louf, R{\'{e}}mi and Barthelemy, Marc},
-doi = {10.1371/journal.pone.0157476},
-eprint = {1511.04268},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Louf, Barthelemy - 2016 - Patterns of Residential Segregation.PDF:PDF},
-journal = {arXiv},
-number = {v1},
-title = {{Patterns of residential segregation}},
-url = {http://arxiv.org/abs/1511.04268},
-volume = {1511.04268},
-year = {2015}
-}
-@book{Condit1998,
-address = {Berlin, Germany, and Georgetown, Texas},
-author = {Condit, Richard},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Condit - 1998 - Tropical Forest Census Plots.pdf:pdf},
-isbn = {3-540-64144-0},
-pages = {1--224},
-publisher = {Springer-Verlag and R. G. Landes Company},
-title = {{Tropical Forest Census Plots}},
-url = {http://ctfs.arnarb.harvard.edu/Public/pdfs/Condit{\_}1998{\_}CensusPlotsmethodsBook.pdf},
-year = {1998}
-}
-@article{Ochiai1957,
-author = {Ochiai, Akira},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ochiai - 1957 - Zoogeographic studies on the soleoid fishes found in Japan and its neighbouring regions.pdf:pdf},
-journal = {Bulletin of the Japanese Society of Scientific Fisheries},
-number = {9},
-pages = {526--530},
-title = {{Zoogeographic studies on the soleoid fishes found in Japan and its neighbouring regions}},
-volume = {22},
-year = {1957}
-}
-@article{Butturi-Gomes2014,
-abstract = {The use of diversity indices is a common practice in studies of community ecology. Historically, the main indices were derived by Shannon and Simpson. Currently, these two indices are recognized as part of families of entropy-based indices, which generally include species richness as another particular case. This paper evaluates the statistical properties of one of these families, the Tsallis index, as dependent on four factors: (i) spatial distribution of individuals; (ii) species-abundance distributions; (iii) sampling method and (iv) the estimator. To do so, we carried out computer simulations. The maximum likelihood estimator under all scenarios produced more biased estimates than the two computationally intensive estimation methods (i.e., Jackknife and bootstrap). The Broken-Stick was the species-abundance distribution that led to lowest bias, particularly in the species richness estimation. Intermediate levels of spatial aggregation of individuals were also related to less biased estimations of diversity. The effect of quadrat size upon the bias of estimation was weak, despite the fact that such sampling method often produces a non-random sample of individuals. On the one hand, the Jackknife method was more accurate than the bootstrap, although both methods have shown poor performances for diversity indices that emphasize species richness. On the other hand, if confidence intervals are needed for individual community samples, the bootstrap is strongly recommended over the Jackknife.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Butturi-Gomes, Davi and Junior, Miguel Petrere and Giacomini, Henrique C and Junior, Paulo De Marco},
-doi = {http://dx.doi.org/10.1016/j.ecolind.2013.10.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Butturi-Gomes et al. - 2014 - Computer intensive methods for controlling bias in a generalized species diversity index.pdf:pdf},
-journal = {Ecological Indicators},
-number = {0},
-pages = {90--98},
-title = {{Computer intensive methods for controlling bias in a generalized species diversity index}},
-url = {http://www.sciencedirect.com/science/article/pii/S1470160X13003750},
-volume = {37, Part A},
-year = {2014}
-}
-@article{Ripley1976,
-abstract = {We show how to build models of random collections of geometrical objects: lines, circles, line segments, etc. This basic problem in stochastic geometry is solved using the theory of point processes on abstract spaces.},
-author = {Ripley, Brian D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1976 - The Foundations of Stochastic Geometry.pdf:pdf},
-journal = {Annals of Probability},
-number = {6},
-pages = {995--998},
-title = {{The Foundations of Stochastic Geometry}},
-url = {https://www.jstor.org/stable/2242958},
-volume = {4},
-year = {1976}
-}
-@article{Marcon2014e,
-author = {Marcon, Eric and Zhang, Zhiyi and H{\'{e}}rault, Bruno},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Zhang, H{\'{e}}rault - 2014 - The Decomposition of Similarity-Based Diversity and its Bias Correction.pdf:pdf},
-journal = {HAL},
-number = {version 3},
-title = {{The Decomposition of Similarity-Based Diversity and its Bias Correction}},
-volume = {00989454},
-year = {2014}
-}
-@article{Veron2016a,
-abstract = {There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary rela- tionships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data-deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data-deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best- vs. worst-case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data-deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data-deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phyloge- netic diversity. We found that this loss could be substantially higher than previ- ously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.},
-author = {Veron, Simon and Penone, Caterina and Clergeau, Philippe and Costa, Gabriel C. and Oliveira, Brunno F. and S{\~{a}}o-Pedro, Vin{\'{i}}cius A. and Pavoine, Sandrine},
-doi = {10.1002/ece3.2390},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Veron et al. - 2016 - Integrating data-deficient species in analyses of evolutionary history loss.pdf:pdf},
-journal = {Ecology and Evolution},
-number = {23},
-pages = {8502--8514},
-title = {{Integrating data-deficient species in analyses of evolutionary history loss}},
-url = {http://doi.wiley.com/10.1002/ece3.2390},
-volume = {6},
-year = {2016}
-}
-@book{Duranton2008a,
-address = {Paris, France.},
-author = {Duranton, Gilles and Martin, Gilles and Mayer, Thierry and Mayneris, Florian},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton et al. - 2008 - Les p{\^{o}}les de comp{\'{e}}titivit{\'{e}}. Que peut-on en attendre.pdf:pdf},
-isbn = {9782728803972},
-publisher = {{\'{E}}ditions Rue d'Ulm, Presses de l'{\'{E}}cole normale sup{\'{e}}rieure},
-title = {{Les p{\^{o}}les de comp{\'{e}}titivit{\'{e}}. Que peut-on en attendre ?}},
-year = {2008}
-}
-@article{Rozendaal2006,
-abstract = {1. The sun-shade acclimation and plasticity of 16 functional leaf traits of 38 tropical tree species were studied in relation to their light demand, maximum adult stature and ontogenetic changes in crown exposure. 2. Species differed significantly in all leaf traits, which explained a large part of the observed variation (average R-2 = 0.72). Light had a significant effect on 12 traits and species showed a similar proportional response to light, indicating that the species ranking in trait performance is largely maintained in different light environments. 3. Specific leaf area, leaf nutrient content and chlorophyll : nitrogen ratio showed the largest plasticity to irradiance. These traits are important for maximizing growth in different light conditions because they are closely linked to the photosynthetic capacity and carbon balance of the plant. 4. Plasticity is generally thought to be greatest for pioneer species that occupy early successional habitats with a large variation in irradiance. This hypothesis was rejected because short-lived pioneers showed the lowest plasticity to irradiance. 5. An alternative hypothesis states that plasticity is largest for tall species that experience large ontogenetic changes in irradiance during their life cycle. Yet plasticity was barely related to adult stature or ontogenetic changes in crown exposure. Short-lived pioneers that experience consistently high light levels did have low plasticity, but shade-tolerant species that experience consistently low light levels had high plasticity. 6. Tropical rainforest species show a large variation in plasticity. Plasticity is a compromise between many factors and constraints, and all of these may explain the observed patterns to some extent.},
-author = {Rozendaal, D. M. A. and Hurtado, V. H. and Poorter, Lourens},
-doi = {10.1111/j.1365-2435.2006.01105.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rozendaal, Hurtado, Poorter - 2006 - Plasticity in leaf traits of 38 tropical tree species in response to light relationships with light.pdf:pdf},
-journal = {Functional Ecology},
-number = {2},
-pages = {207--216},
-title = {{Plasticity in leaf traits of 38 tropical tree species in response to light; relationships with light demand and adult stature}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2006.01105.x/abstract},
-volume = {20},
-year = {2006}
-}
-@article{Marcon2014c,
-abstract = {entropart is a package for R designed to estimate diversity based on HCDT entropy or similarity-based entropy. It allows calculating species-neutral, phylogenetic and functional entropy and diversity, partitioning them and correcting them for estimation bias.},
-author = {Marcon, Eric and H{\'{e}}rault, Bruno},
-doi = {10.18637/jss.v067.i08},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, H{\'{e}}rault - 2015 - entropart, an R Package to Measure and Partition Diversity.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {8},
-pages = {1--26},
-title = {{entropart, an R Package to Measure and Partition Diversity}},
-url = {http://cran.r-project.org/package=entropart},
-volume = {67},
-year = {2015}
-}
-@article{Loh2005,
-abstract = {The Living Planet Index was developed to measure the changing state of the world's biodiversity over time. It uses time-series data to calculate average rates of change in a large number of populations of terrestrial, freshwater and marine vertebrate species. The dataset contains about 3000 population time series for over 1100 species. Two methods of calculating the index are outlined: the chain method and a method based on linear modelling of log-transformed data. The dataset is analysed to compare the relative representation of biogeographic realms, ecoregional biomes, threat status and taxonomic groups among species contributing to the index. The two methods show very similar results: terrestrial species declined on average by 25{\%} from 1970 to 2000. Birds and mammals are over-represented in comparison with other vertebrate classes, and temperate species are over-represented compared with tropical species, but there is little difference in representation between threatened and non-threatened species. Some of the problems arising from over-representation are reduced by the way in which the index is calculated. It may be possible to reduce this further by post-stratification and weighting, but new information would first need to be collected for data-poor classes, realms and biomes.},
-author = {Loh, Jonathan and Green, Rhys E. and Ricketts, Taylor and Lamoreux, John and Jenkins, Martin and Kapos, Valerie and Randers, Jorgen},
-doi = {10.1098/rstb.2004.1584},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loh et al. - 2005 - The Living Planet Index using species population time series to track trends in biodiversity.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1454},
-pages = {289--295},
-title = {{The Living Planet Index: using species population time series to track trends in biodiversity.}},
-volume = {360},
-year = {2005}
-}
-@article{Cadotte2012,
-abstract = {Ecosystem stability in variable environments depends on the diversity of form and function of the constituent species. Species phenotypes and ecologies are the product of evolution, and the evolutionary history represented by co-occurring species has been shown to be an important predictor of ecosystem function. If phylogenetic distance is a surrogate for ecological differences, then greater evolutionary diversity should buffer ecosystems against environmental variation and result in greater ecosystem stability. We calculated both abundance-weighted and unweighted phylogenetic measures of plant community diversity for a long-term biodiversity-ecosystem function experiment at Cedar Creek, Minnesota, USA. We calculated a detrended measure of stability in aboveground biomass production in experimental plots and showed that phylogenetic relatedness explained variation in stability. Our results indicate that communities where species are evenly and distantly related to one another are more stable compared to communities where phylogenetic relationships are more clumped. This result could be explained by a phylogenetic sampling effect, where some lineages show greater stability in productivity compared to other lineages, and greater evolutionary distances reduce the chance of sampling only unstable groups. However, we failed to find evidence for similar stabilities among closely related species. Alternatively, we found evidence that plot biomass variance declined with increasing phylogenetic distances, and greater evolutionary distances may represent species that are ecologically different (phylogenetic complementarity). Accounting for evolutionary relationships can reveal how diversity in form and function may affect stability.},
-annote = {ISI Document Delivery No.: 985WY
-Times Cited: 11
-Cited Reference Count: 56
-Cadotte, Marc W. Dinnage, Russell Tilman, David
-Nserc [386151]
-We thank the organizers of this Special Issue for inviting us to contribute a paper, and we are greatful to two anonymous reviewers for many helpful comments. M. W. Cadotte is generously supported by an NSERC discovery grant (386151).
-Ecological soc amer
-Washington
-S},
-author = {Cadotte, Marc W. and Dinnage, Russel and Tilman, David},
-doi = {10.1890/11-0426.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte, Dinnage, Tilman - 2012 - Phylogenetic diversity promotes ecosystem stability.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {S223--S233},
-title = {{Phylogenetic diversity promotes ecosystem stability}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/11-0426.1/abstract},
-volume = {93},
-year = {2012}
-}
-@article{Briant2010,
-abstract = {This paper evaluates, in the context of economic geography estimates, the magnitude of the distortions arising from the choice of a specific zoning system, which is also known as the Modifiable Areal Unit Problem (MAUP). We undertake three standard economic geography exercises (the analysis of spatial concentration, agglomeration economies, and trade determinants), using various French zoning systems differentiated according to the size and shape of their spatial units. While size might matter, especially when the dependent variable of a regression is not aggregated in the same way as the explanatory variables and/or the zoning system involves large spatial units, shape does so much less. In any case, both dimensions are of secondary importance compared to specification issues.},
-author = {Briant, Anthony and Combes, Pierre-Philippe and Lafourcade, Miren},
-doi = {10.1016/j.jue.2009.09.014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Briant, Combes, Lafourcade - 2010 - Dots to boxes Do the Size and Shape of Spatial Units Jeopardize Economic Geography Estimations.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {3},
-pages = {287--302},
-title = {{Dots to boxes: Do the Size and Shape of Spatial Units Jeopardize Economic Geography Estimations?}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119009000813},
-volume = {67},
-year = {2010}
-}
-@article{Whitfeld2014,
-abstract = {Much of the world's tropical forests have been affected by anthropogenic disturbance. These forests are important biodiversity reservoirs whose diversity, structure and function must be characterized across the successional sequence. We examined changes in structure and diversity along a successional gradient in the lowlands of New Guinea. To do this, we measured and identified all stems ≥5 cm diameter in 19 0.25 ha plots ranging in age from 3 to {\textgreater}50 yr since disturbance. We also measured plant functional traits related to establishment, performance, and competitive ability. In addition, we examined change in forest structure, composition, species diversity, and functional diversity through succession. By using rarefaction to estimate functional diversity, we compared changes in functional diversity while controlling for associated differences in stem and species density. Basal area and species density increased with stand age while stem density was highest in intermediate secondary forests. Species composition differed strongly between mature and secondary forests. As forests increased in basal area, community-weighted mean wood density and foliar carbon increased, whereas specific leaf area and pro- portion of stems with exudate decreased. Foliar nitrogen peaked in medium-aged forests. Functional diversity was highest in mature for- ests, even after accounting for differences in stem and species diversity. Our study represents one of the first attempts to document successional changes in New Guinea's lowland forest. We found robust evidence that as succession proceeds, communities occupy a greater range of functional trait space even after controlling for stem and species density. High functional diversity is important for eco- logical resiliency in the face of global change.},
-author = {Whitfeld, Timothy J. S. and Lasky, Jesse R. and Damas, Kipiro and Sosanika, Gibson and Molem, Kenneth and Montgomery, Rebecca A.},
-doi = {10.1111/btp.12136},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whitfeld et al. - 2014 - Species Richness, Forest Structure, and Functional Diversity During Succession in the New Guinea Lowlands.pdf:pdf},
-journal = {Biotropica},
-number = {5},
-pages = {538--548},
-title = {{Species Richness, Forest Structure, and Functional Diversity During Succession in the New Guinea Lowlands}},
-url = {http://doi.wiley.com/10.1111/btp.12136},
-volume = {46},
-year = {2014}
-}
-@article{Zhang1995,
-abstract = {Small-scale species dynamics in semi-arid steppe vegetation under grazing and recovering from long-term graz- ing were followed during five years. Most species succes- sively increased their frequency during the study period, whereas some early successional species decreased in fre- quency. Perennial Artemisia spp. dominated the vegetation and showed low mobility, whereas small annual or short-lived perennial species had a lower frequency and higher mobility. Significant associations between species were few.},
-author = {Zhang, Wei and Skarpe, Christina},
-doi = {10.2307/3236357},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Skarpe - 1995 - Small-scale species dynamics in semi-arid steppe vegetation in Inner Mongolia.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {583--592},
-title = {{Small-scale species dynamics in semi-arid steppe vegetation in Inner Mongolia}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236357/abstract},
-volume = {6},
-year = {1995}
-}
-@article{Jimenez2016,
-abstract = {The soft cardinality function generalizes the concept of counting measure of the classic cardinality of sets. This function provides an intuitive measure of the amount of elements in a collection (i.e. a set or a bag) exploiting the similarities among them. Although soft cardinality was first proposed in an ad-hoc way, it has been successfully used in various tasks in the field of natural language processing. In this paper, a formal definition of soft cardinality is proposed together with an analysis of its boundaries, monotonicity property and a method for constructing similarity functions. Additionally, an empirical evaluation of the model was carried out using synthetic data.},
-author = {Jimenez, Sergio and Gonzalez, Fabio A. and Gelbukh, Alexander},
-doi = {10.1016/j.ins.2016.06.012},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jimenez, Gonzalez, Gelbukh - 2016 - Mathematical properties of soft cardinality Enhancing Jaccard , Dice and cosine similarity measures.pdf:pdf},
-journal = {Information Sciences},
-pages = {373--389},
-title = {{Mathematical properties of soft cardinality : Enhancing Jaccard , Dice and cosine similarity measures with element-wise distance}},
-url = {http://dx.doi.org/10.1016/j.ins.2016.06.012},
-volume = {367-368},
-year = {2016}
-}
-@article{Kincses2013,
-abstract = {Our study aims at describing the spatial structure of Europe with spatial moving average, potential model and the bidimensional regression analysis based on gravity model. Many theoretical and practical works aim at describing the spatial structure of Europe. Partly zones, axes and formations, partly polycentric models appear in the literature. We illustrate their variegation by listing, without any claim to completeness (since that could be the subject of another study), a part of them. Based on our examinations, the engraving of the structures that we described can be seen. The position of the core area of EU countries clearly justifies the banana shape and in relation to it, the catching up regions take shape in several areas.},
-annote = {ISI Document Delivery No.: 245RW
-Times Cited: 0
-Cited Reference Count: 28
-Kincses, Aron Nagy, Zoltan Toth, Geza
-New Hungarian Development Plan [TAMOP-4.2.1.B-10/2/KONV-2010-0001]; European Union; European Social Fund
-The described work was carried out as part of the TAMOP-4.2.1.B-10/2/KONV-2010-0001 project in the framework of the New Hungarian Development Plan. The realization of this project is supported by the European Union, co-financed by the European Social Fund.
-Geografski inst antona melika zrc sazu
-Ljubljana},
-author = {Kincses, {\'{A}}ron and Nagy, Zolt{\'{a}}n and T{\'{o}}th, G{\'{e}}za},
-doi = {10.3986/ags53103},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kincses, Nagy, Toth - 2013 - The spatial structure of Europe considered by various models.pdf:pdf},
-journal = {Acta Geographica Slovenica-Geografski Zbornik},
-number = {1},
-pages = {44--60},
-title = {{The spatial structure of Europe considered by various models}},
-url = {http://www.academia.edu/3850464/The{\_}spatial{\_}structure{\_}of{\_}Europe{\_}considered{\_}by{\_}various{\_}models},
-volume = {53},
-year = {2013}
-}
-@article{Bastias2017,
-abstract = {Disentangling the mechanisms that shape community assembly across diversity gradients is a central matter in ecology. While many studies have explored community assembly through species average trait values, there is a growing understanding that intraspecific trait variation (ITV) can also play a critical role in species coexistence. Classic biodiversity theory hypothesizes that higher diversity at species-rich sites can arise from narrower niches relative to species-poor sites, which would be reflected in reduced ITV as species richness increases. To explore how ITV in woody plant communities changes with species richness, we compiled leaf trait data (leaf size and specific leaf area) in a total of 521 woody plant species from 21 forest communities that differed dramatically in species richness, ranging from boreal to tropical rainforests. At each forest, we assessed ITV as an estimate of species niche breadth and we quantified the degree of trait overlap among co-occurring species as a measure of species functional similarity. We found ITV was relatively invariant across the species richness gradient. In addition, we found that species functional similarity increased with diversity. Contrary to the expectation from classic biodiversity theory, our results rather suggest that neutral processes or equalizing mechanisms can be acting as potential drivers shaping community assembly in hyperdiverse forests.},
-author = {Bastias, Cristina C. and Fortunel, Claire and Valladares, Fernando and Baraloto, Christopher and Benavides, Raquel and Cornwell, William and Markesteijn, Lars and de Oliveira, Alexandre A. and Sansevero, Jeronimo B. B. and Vaz, Marcel C. and Kraft, Nathan J. B.},
-doi = {10.1371/journal.pone.0172495},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bastias et al. - 2017 - Intraspecific leaf trait variability along a boreal-to-tropical community diversity gradient.pdf:pdf},
-journal = {Plos One},
-number = {2},
-pages = {e0172495},
-title = {{Intraspecific leaf trait variability along a boreal-to-tropical community diversity gradient}},
-url = {http://dx.plos.org/10.1371/journal.pone.0172495},
-volume = {12},
-year = {2017}
-}
-@article{Greig-Smith1952,
-abstract = {Artificial 'communities' of discs have been constructed and sampled by random throws of quadrats of different sizes and by a grid of contiguous quadrats. The use of a grid opens the way to more detailed study of the nature of the non-random distribution of species in the field, especially to the detection of mosaic patterns not normally revealed by subjective methods.},
-author = {Greig-Smith, Peter},
-doi = {10.1093/oxfordjournals.aob.a083317},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Greig-Smith - 1952 - The use of random and contiguous quadrats in the study of the structure of plant communities.pdf:pdf},
-journal = {Annals of Botany},
-number = {62},
-pages = {293--316},
-title = {{The use of random and contiguous quadrats in the study of the structure of plant communities}},
-volume = {16},
-year = {1952}
-}
-@book{Balee1994,
-author = {Bal{\'{e}}e, William},
-isbn = {10: 0231074840},
-publisher = {Columbia University Press},
-title = {{Footprints of the Forest: Ka'Apor Ethnobotany - The Historical Ecology of Plant Utilization by an Amazonian People (Biology and Resource Management in the Tropics)}},
-year = {1994}
-}
-@book{Brocard2011,
-address = {New York},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Borcard, Daniel and Gillet, Fran{\c{c}}ois and Legendre, Pierre},
-booktitle = {Applied Spatial Data Analysis with R},
-doi = {10.1007/978-1-4419-7976-6},
-eprint = {arXiv:1011.1669v3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Borcard, Gillet, Legendre - 2011 - Numerical Ecology with R.pdf:pdf},
-isbn = {978-1-4419-7975-9},
-issn = {9780387938363},
-pmid = {22057480},
-publisher = {Springer},
-title = {{Numerical Ecology with R}},
-year = {2011}
-}
-@phdthesis{Reynolds1998,
-abstract = {The Modifiable Area Unit Problem (MAUP) has been discussed in the spatial analysis literature since the 1930's, but it is the recent surge in the availability of desktop computing power and Geographical Information Systems software that have caused both a resurgence of interest in the problem and a greater need to learn more about it. Many spatial datasets are collected on a fine resolution (i.e. a large number of small spatial units) but, for the sake of privacy and/or size concerns, are released only after being spatially aggregated to a coarser resolution (i.e. a smaller number of larger spatial units). The chief example of this process is census data which are collected from every household, but released only at the Enumeration Area or Census Tract level of spatial resolution. When values are averaged over the process of aggregation, variability in the dataset is lost and values of statistics computed at the different resolutions will be different; this change is called the scale effect. One also gets different values of statistics depending on how the spatial aggregation occurs; this variability is called the zoning effect. The purpose of studying the MAUP is to try to estimate the true values of the statistics at the original level of spatial resolution. Knowing these would allow researchers to attempt to make estimates of the data values using either synthetic spatial data generators like the one described in this thesis or by other techniques.},
-address = {Toronto},
-author = {Reynolds, Harold David},
-booktitle = {Graduate Department of Geography},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reynolds - 1998 - The Modifiable Area Unit Problem Empirical Analysis by Statistical Simulation.pdf:pdf},
-publisher = {University of Toronto},
-title = {{The Modifiable Area Unit Problem: Empirical Analysis by Statistical Simulation}},
-year = {1998}
-}
-@article{ODriscoll2000,
-abstract = {Analysis of simulated data showed that potential contact statistics could be used to describe spatial pattern in sample density data. Potential contact is a new method, analogous to Ripley's K function for mapped point pattern analysis. Potential contact can be used to describe spatial pattern and association over a range of scales without grouping data and is robust against the presence of zeros. The statistical output is ecologically interpretable, as a measure of the degree of contact between individuals. This new technique was applied to examine changes in the spatial distribution of Atlantic cod (Gadus morhua) off Newfoundland, Canada, from 1985 to 1994, a period that encompassed a collapse of the cod stock. Sample data from bottom-trawl surveys indicated that cod were aggregated in patches with dimensions of 100-250 km. During the period of cod decline in the 1990s, spatial structure changed in three ways: the number of patches decreased, patch size shrank, and contact with conspecifics at small (10-20 km) scales fell. Cod were broadly associated with capelin (Mallotus villosus), a major prey species. Spatial distribution of capelin changed over the same time period as changes in cod distribution, and there was no evidence that contact between cod and capelin decreased.},
-annote = {Article
-English
-CAN J FISHERIES AQUAT SCI
-327EM},
-author = {O'Driscoll, Richard L. and Schneider, David C. and Rose, George A. and Lilly, George R.},
-doi = {10.1139/f05-192},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/O'Driscoll et al. - 2000 - Potential contact statistics for measuring scale-dependent spatial pattern and association an example of nort.pdf:pdf},
-journal = {Canadian Journal of Fisheries and Aquatic Sciences},
-number = {7},
-pages = {1355--1368},
-title = {{Potential contact statistics for measuring scale-dependent spatial pattern and association: an example of northern cod (Gadus morhua) and capelin (Mallotus villosus)}},
-url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f00-079{\#}.V0GzeOSTOJU},
-volume = {57},
-year = {2000}
-}
-@article{Lajoie2015,
-abstract = {Intraspecific trait variation (ITV) plays a potentially important role in determining functional community composition across environmental gradients. However, the importance of ITV varies greatly among studies, and we lack a coherent understanding of the contexts under which to expect a high versus low contribution of ITV to trait-environment matching among communities. Here we first elaborate a novel conceptual framework posing specific hypotheses and predictions about the environmental and ecological contexts underlying the contribution of ITV to community trait turnover. We then empirically test these predictions in understory herbaceous plant communities in a montane environment, for 3 functional traits (flowering phenology, specific leaf area and height). We found that different components of trait variation mapped onto different environmental axes, specifically reporting a greater contribution of ITV along non-climatic axes (e.g., soil properties, light) than along the main climatic axis (i.e., ele...},
-author = {Lajoie, Genevi{\`{e}}ve and Vellend, Mark},
-doi = {10.1890/15-0156.1.sm},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lajoie, Vellend - 2015 - Understanding context dependence in the contribution of intraspecific variation to community trait-environment.pdf:pdf},
-journal = {Ecology},
-number = {11},
-pages = {2912--2922},
-title = {{Understanding context dependence in the contribution of intraspecific variation to community trait-environment matching}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/15-0156.1/abstract},
-volume = {96},
-year = {2015}
-}
-@incollection{Jensen2006,
-address = {Washington},
-author = {Jensen, B. J. and Kletzer, L. G.},
-booktitle = {Brookings Trade Forum: 2005. Offshoring White-Collar Work – The Issues and the Implications},
-editor = {Brainard, L and Collins, S M},
-pages = {75--134},
-publisher = {Brookings Institution Press},
-title = {{Tradable Services: Understanding the Scope and Impact of Services Offshoring}},
-url = {http://www.brookings.edu/press/Journals/2006/brookingstradeforum2005.aspx},
-year = {2006}
-}
-@article{Vamosi2009,
-abstract = {The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty-three of 39 studies (59{\%}) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over-represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one-dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.},
-author = {Vamosi, S. M. and Heard, S. B. and Vamosi, J. C. and Webb, Campbell O.},
-doi = {10.1111/j.1365-294X.2008.04001.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vamosi et al. - 2009 - Emerging patterns in the comparative analysis of phylogenetic community structure.pdf:pdf},
-journal = {Molecular ecology},
-number = {4},
-pages = {572--92},
-title = {{Emerging patterns in the comparative analysis of phylogenetic community structure.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/19037898},
-volume = {18},
-year = {2009}
-}
-@book{Greene2003,
-address = {Upper Saddle River},
-author = {Greene, William H.},
-edition = {5th ed.},
-publisher = {Prentice Hall},
-title = {{Econometric Analysis}},
-year = {2003}
-}
-@article{Baddeley2005,
-author = {Baddeley, Adrian J. and Turner, Rolf},
-doi = {10.18637/jss.v012.i06},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, Turner - 2005 - Spatstat an R package for analyzing spatial point patterns.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {6},
-pages = {1--42},
-title = {{Spatstat: an R package for analyzing spatial point patterns}},
-url = {https://www.jstatsoft.org/article/view/v012i06},
-volume = {12},
-year = {2005}
-}
-@article{Campos2009,
-abstract = {ab stra ct During the past decades several biodiversity indices have been proposed and employed in ecological literature. Although each one has been partially justified on practical or quasi- theoretical grounds, recommendations of ecological theorists differ from describing which index to use. The goal of this article is to introduce a new index for measuring biological diversity that is sensitive to the number of different species (species richness, S), and the relative abundance of them. We take advantage from the mathematical relation between Simpson index and the geometrical concept of a S-dimensional sphere of radius r, where r is the square root of the Simpson index. Full applications of the method are developed, first with hypothetical communities and then with real data for 1761 specimens of 82 weevil species collected in several forest types [Ohsawa, M., 2005. Species richness and composi- tion of Curculionidae (Coleopters) in a conifer plantation, secondary forest, and old-growth forest in the central mountainous region of Japan.},
-author = {Campos, Di{\'{o}}genes and Isaza, Jos{\'{e}} Fernando},
-doi = {10.1016/j.ecolind.2008.07.007},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Campos, Isaza - 2009 - A geometrical index for measuring species diversity.pdf:pdf},
-journal = {Ecological Indicators},
-number = {4},
-pages = {651--658},
-title = {{A geometrical index for measuring species diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X08000848},
-volume = {9},
-year = {2009}
-}
-@article{Reich1999,
-abstract = {Convergence in interspecific leaf trait relationships across diverse taxonomic groups and biomes would have important evolutionary and ecological implications. Such convergence has been hypothesized to result from trade-offs that limit the combination of plant traits for any species. Here we address this issue by testing for biome differences in the slope and intercept of interspecific relationships among leaf traits: longevity, net photosynthetic capacity (A(max)), leaf diffusive conductance (G(s)), specific leaf area (SLA), and nitrogen (N) status, for more than 100 species in six distinct biomes of the Americas. The six biomes were: alpine tundra-subalpine forest ecotone, cold temperate forest-prairie ecotone, montane cool temperate forest, desert shrubland, subtropical forest, and tropical rain forest. Despite large differences in climate and evolutionary history, in all biomes mass-based leaf N (N-mass), SLA, G(s), and A(max) were positively related to one another and decreased with increasing leaf life span. The relationships between pairs of leaf traits exhibited similar slopes among biomes, suggesting a predictable set of scaling relationships key leaf morphological, chemical, and metabolic traits that are replicated globally among terrestrial ecosystems regardless of biome or vegetation type. However, the intercept (i.e., the overall elevation of regression lines) of relationships between pairs of leaf traits usually differed among biomes. With increasing aridity across sites, species had greater A(max) for a given level of G(s) and lower SLA for any given leaf life span. Using principal components analysis, most variation among species was explained by an axis related to mass-based leaf traits (A(max) N, and SLA) while a second axis reflected climate, G(s), and other area-based leaf traits.},
-author = {Reich, Peter B. and Ellsworth, D. S. and Walters, M. B. and Vose, J. M. and Gresham, C. and Volin, J. C. and Bowman, W. D.},
-doi = {10.1890/0012-9658(1999)080[1955:GOLTRA]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Reich et al. - 1999 - Generality of leaf trait relationships A test across six biomes.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1955--1969},
-title = {{Generality of leaf trait relationships: A test across six biomes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(1999)080[1955:GOLTRA]2.0.CO;2/abstract},
-volume = {80},
-year = {1999}
-}
-@article{Moeur1997,
-abstract = {Stem-mapped plots in old-growth forests of western hemlock (Tsuga heterophylla) and western redcedar (Thuja plicata) in northern Idaho, USA were analyzed using Ripley's K(d) function, nearest-neighbor function, and influence zone analyses. A conceptual model of old-growth forest development was formulated from the spatial pattern analyses, to guide the development of a mathematical model. In the conceptual model, cohorts of seedlings begin life established in clusters associated with canopy gaps created by the deaths of overstory trees. Then, as the trees within clusters increase in size, they begin to compete with their immediate neighbors. Density-dependent mortality thins the clusters and increases the distance between neighboring trees. Over time, this self-thinning behavior tends to drive stand spatial patterns from aggregation towards regular spacing as trees get larger or increase in competitive status. Preliminary results from a dynamic point process model are presented. The approach simulates the regeneration of seedlings in gaps and the dynamic spatial patterns resulting from competitive interactions between neighboring trees as a sequence of point processes. Main features of the model are stochastic assignment of gapmaker trees, a Poisson cluster process for regeneration establishment, and a progressive simple inhibition process for competition between neighboring trees. The model produces spatial patterns for regeneration and adult trees consistent with the conceptual model and with patterns observed in the field data. Refinements designed to improve model realism are discussed.},
-author = {Moeur, Melinda},
-doi = {10.1016/S0378-1127(96)03976-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moeur - 1997 - Spatial models of competition and gap dynamics in old-growth Tsuga heterophylla Thuja plicata forests(2).pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {175--186},
-title = {{Spatial models of competition and gap dynamics in old-growth Tsuga heterophylla / Thuja plicata forests}},
-url = {http://www.sciencedirect.com/science/article/pii/S037811279603976X},
-volume = {94},
-year = {1997}
-}
-@article{Schmera2009,
-abstract = {Functional diversity is regarded as a key in understanding the link between ecosystem function and biodiversity, but its measurement is rather problematic. The two widely used continuous measures are the dendrogram-based measure (DBM) and the functional attribute diversity (FAD). In contrast to DBM, FAD does not require the knowledge of the entire species pool before the analysis, and hence FAD is a more ideal tool for measuring functional diversity. However, the original form of FAD and its variants have several undesirable properties. Here, we suggest a modified FAD (denoted by MFAD), which—as illustrated by artificial and actual data sets—allows calculating functional diversity without violating the twinning and monotonicity criteria such that the number of species collected is compensated for. These requirements are met by replacing the original species by so-called functional species and then by dividing FAD by the number of functional units. Accordingly, MFAD measures the dispersion of species in the functional traits space so that MFAD values for different communities can directly be compared if the same set of functional traits is used. Finally, using data of two freshwater communities (caddisfly and riverine fish), we evaluate the change of species richness and functional diversity in relation to sampling effort (sample unit size). We found that functional diversity is a better and more reliable community descriptor than species richness in a sense that it converges to the maximum faster in the function of sampling effort.},
-author = {Schmera, D{\'{e}}nes and Erős, Tibor and Podani, J{\'{a}}nos},
-doi = {10.1007/s10452-007-9152-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schmera, Erős, Podani - 2009 - A measure for assessing functional diversity in ecological communities.pdf:pdf},
-journal = {Aquatic Ecology},
-number = {1},
-pages = {157--167},
-title = {{A measure for assessing functional diversity in ecological communities}},
-url = {http://dx.doi.org/10.1007/s10452-007-9152-9},
-volume = {43},
-year = {2009}
-}
-@article{Allard1997,
-abstract = {This article addresses the problem of estimating the support domain of a bounded point process in presence of background noise. This situation occurs, for example, in the detection of a minefield from aerial observations. A maximum likelihood estimator for a mixture of uniform point processes is derived using a natural partition of the space defined by the data themselves: the Vorono{\"{i}} tessellation. The methodology is tested on simulations and compared to a model-based clustering technique.},
-author = {Allard, Denis and Fraley, Chris},
-doi = {10.1080/01621459.1997.10473670},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Allard, Fraley - 1997 - Nonparametric Maximum Likelihood Estimation of Features in Spatial Point Processes Using Voronoi Tessellation.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {440},
-pages = {1485--1493},
-title = {{Nonparametric Maximum Likelihood Estimation of Features in Spatial Point Processes Using Voronoi Tessellation}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/01621459.1997.10473670},
-volume = {92},
-year = {1997}
-}
-@article{Ghorbani2013,
-abstract = {In this paper we introduce an instance of the well-know Neyman–Scott cluster process model with clusters having a long tail behaviour. In our model the offspring points are distributed around the parent points according to a circular Cauchy distribution. Using a modified Cram{\'{e}}r-von Misses test statistic and the simulated pointwise envelopes it is shown that this model fits better than the Thomas process to the frequently analyzed long-leaf pine data-set.},
-author = {Ghorbani, Mohammad},
-doi = {10.1007/s00184-012-0411-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ghorbani - 2013 - Cauchy cluster process.pdf:pdf},
-journal = {Metrika},
-number = {5},
-pages = {697--706},
-title = {{Cauchy cluster process}},
-url = {http://dx.doi.org/10.1007/s00184-012-0411-y},
-volume = {76},
-year = {2013}
-}
-@misc{JournalofficieldelaRepubliquefrancaise2009a,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{D{\'{e}}cret n° 2009-1065 du 28 ao{\^{u}}t 2009 modifiant certaines dispositions relatives au compte {\'{e}}pargne-temps dans la fonction publique de l'Etat et dans la magistrature}},
-url = {http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000021006639},
-year = {2009}
-}
-@article{Forget1999,
-abstract = {The spatial distribution of 2 rain forest tree species, Carapa procera (Meliaceae) and Vouacapoua americana (Caesalpiniaceae), was analysed within and between 2 plots (6.25 and 25 ha) at Paracou, French Guiana, using census data from 1992 and 1994. The L(d) function was used to characterize spatial patterns, and the Lij(d) intertype to study independancy between young and adult trees. Although both species are dispersed by caviomorph rodents within short distances (approx equal to 10- 20 m) of parent tree crowns, the analysis of tree positions indicated different spatial patterns between species depending on soil drainage characteristics. V. americana exhibited a strongly aggregated spatial distribution, while C. procera was less likely to depart from complete spatial randomness (CSR). A complex distribution, sometimes clustered in areas with hydromorphic soils (swamps and around streams) and sometimes very near CSR outside these areas, characterized the C. procera population. When C. procera tree aggregation occurred, a slight attraction between juveniles and adults was observed. The aggregation of V. americana trees was observed at different levels depending on the scale of investigation. Within small plots a first level of aggregation with short distance radii of approx equal to 10-25 m giving small clusters, and a second level composed of small clusters aggregated at approx equal to 40-50 m distance radius, were observed. A third level of aggregation was suggested by analysing the tree population at the larger scale (25 ha) whose boundaries outside the plot were not delimited. Aggregation of V. americana trees at all levels was enhanced by a strong attraction between juveniles and adults. Results are discussed in relation to seed and seedling ecology, especially with regard to seedling and sapling gap- dependence and soil drainage, which it is suggested affected the recruitment of juvenile trees, and therefore final tree spatial pattern.},
-author = {Forget, Pierre-Michel and Mercier, Fran{\c{c}}ois and Collinet, Fr{\'{e}}d{\'{e}}rique},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Forget, Mercier, Collinet - 1999 - Spatial patterns of two rodent-dispersed rain forest trees Carapa procera (Meliaceae) and Vouacapoua.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {3},
-pages = {301--313},
-title = {{Spatial patterns of two rodent-dispersed rain forest trees Carapa procera (Meliaceae) and Vouacapoua americana (Caesalpiniaceae) at Paracou, French Guiana}},
-url = {https://www.cambridge.org/core/journals/journal-of-tropical-ecology/article/spatial-patterns-of-two-rodentdispersed-rain-forest-trees-carapa-procera-meliaceae-and-vouacapoua-americana-caesalpiniaceae-at-paracou-french-guiana/E6702DE158FCB5A05C658CD8D499D1},
-volume = {15},
-year = {1999}
-}
-@article{Griffith2016,
-abstract = {The observation that species may be positively or negatively associated with each other is at least as old as the debate surrounding the nature of community structure which began in the early 1900's with Gleason and Clements. Since then investigating species co-occurrence patterns has taken a central role in understanding the causes and consequences of evolution, history, coexistence mechanisms, competition, and environment for community structure and assembly. This is because co-occurrence among species is a measurable metric in community datasets that, in the context of phylogeny, geography, traits, and environment, can sometimes indicate the degree of competition, displacement, and phylogenetic repulsion as weighed against biotic and environmental effects promoting correlated species distributions. Historically, a multitude of different co-occurrence metrics have been developed and most have depended on data randomization procedures to produce null distributions for significance testing. Here we improve upon and present an R implementation of a recently published model that is metric-free, distribution-free, and randomization-free. The R package, cooccur, is highly accessible, easily integrates into common analyses, and handles large datasets with high performance. In the article we develop the package's functionality and demonstrate aspects of co-occurrence analysis using three sample datasets},
-author = {Griffith, Daniel M. and Veech, Joseph A. and Marsh, Charles J.},
-doi = {10.18637/jss.v069.c02},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Griffith, Veech, Marsh - 2016 - cooccur Probabilistic Species Co-Occurrence Analysis in R.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {Code Snippet 2},
-pages = {1--17},
-title = {{cooccur : Probabilistic Species Co-Occurrence Analysis in R}},
-url = {http://www.jstatsoft.org/v69/c02/},
-volume = {69},
-year = {2016}
-}
-@incollection{Sweeney2002,
-abstract = {Spatial externalities among businesses, though notoriously difficult to measure, are a central concern in urban and regional economics. Traditionally they - along with closely related concepts such as agglomeration economies - have been studied empirically with hedonic models, production and cost functions, and simplified growth models. More recently, researchers have begun using direct measures of proximity among businesses to shed light on the influence of externalities on industrial location, regional growth, and localized technological change. The shift has been aided by an explosion in spatially-referenced economic data, advances in spatial statistics, and the advent of affordable and user-friendly GIS and related software. As existing indicators of concentration and spatial association have been adapted for the economic domain and new ones developed, the pool of measures useful for business location research generally, and externalities more specifically, has expanded. In this chapter, we systematically review and compare a set of leading indicators of business co-location using standard data sets and evaluation criteria. Ultimately, our aim is to assess the capabilities and limits of the measures for understanding spatial business externalities. More generally, we discuss a number of common challenges associated with drawing inferences from cross-sectional spatial data.},
-author = {Sweeney, Stuart H. and Feser, Edward J.},
-booktitle = {Spatially Integrated Social Science: Examples in Best Practice},
-chapter = {12},
-editor = {Goodchild, M.F. and Janelle, D.G.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sweeney, Feser - 2002 - Business location and spatial externalities Tying concepts to measures.pdf:pdf},
-publisher = {Oxford University Press},
-title = {{Business location and spatial externalities: Tying concepts to measures}},
-url = {http://www.planning.unc.edu/facstaff/faculty/feserDocs.htm},
-year = {2004}
-}
-@article{Adler2013,
-abstract = {Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait-dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait-based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait-based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within-community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait-based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.},
-author = {Adler, Peter B. and Fajardo, Alex and Kleinhesselink, Andrew R. and Kraft, Nathan J. B.},
-doi = {10.1111/ele.12157},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Adler et al. - 2013 - Trait-based tests of coexistence mechanisms.pdf:pdf},
-journal = {Ecology Letters},
-number = {10},
-pages = {1294--1306},
-title = {{Trait-based tests of coexistence mechanisms}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12157/abstract},
-volume = {16},
-year = {2013}
-}
-@article{Faust2012,
-abstract = {Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.},
-author = {Faust, Karoline and Raes, Jeroen},
-doi = {10.1038/nrmicro2832},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faust, Raes - 2012 - Microbial interactions from networks to models.pdf:pdf},
-journal = {Nature Reviews Microbiology},
-number = {8},
-pages = {538--550},
-title = {{Microbial interactions: from networks to models}},
-url = {http://dx.doi.org/10.1038/nrmicro2832},
-volume = {10},
-year = {2012}
-}
-@article{Schweizog2014,
-abstract = {The analysis of the location patterns of economic activities in both Europe and the US has been addressed in an extensive literature dependent on increasingly more sophisticated techniques that arguably reframe debate away from the policy questions in focus and towards debate on the complex empirical techniques that seem to be in vogue at any given time. In part this has been a response to some clear shortcomings in the use of simple locational Gini coefficients. It is argued herein that simple index approaches can still retain value if augmented with intuitive reading of some relevant maps. An example of the utility of this approach is provided in relation to the location patterns of four exemplar manufacturing industries in the EU and USA.},
-author = {Schweizog, Robert and Collins, Alan},
-doi = {10.1111/tesg.12084},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schweizog, Collins - 2014 - A Simple Location Index Plus Some Maps and no Apologies Back to Basics on the Development of Links Between E.pdf:pdf},
-journal = {Tijdschrift voor economische en sociale geografie},
-number = {1},
-pages = {17--35},
-title = {{A Simple Location Index Plus Some Maps and no Apologies: Back to Basics on the Development of Links Between Economic Integration and Spatial Concentration of Industries}},
-url = {http://doi.wiley.com/10.1111/tesg.12084},
-volume = {106},
-year = {2014}
-}
-@misc{MENESR2008,
-author = {MENESR},
-title = {{Le cahier de laboratoire national, comment l'utiliser ?}},
-url = {https://intranet.inra.fr/mission{\_}qualite/content/download/2935/29766/version/1/file/CdL{\_}Pourquoi{\_}150206.pdf},
-year = {2008}
-}
-@article{Acs1991,
-author = {Acs, Zoltan J. and Audretsch, David B. and Feldman, Maryann P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Acs, Audretsch, Feldman - 1991 - Real Effects of Academic Research Comment.pdf:pdf},
-journal = {The American Economic Review},
-number = {1},
-pages = {363--367},
-title = {{Real Effects of Academic Research: Comment}},
-url = {http://www.jstor.org/stable/2117624},
-volume = {82},
-year = {1991}
-}
-@article{Mugabushaka2016,
-abstract = {In bibliometrics, interdisciplinarity is often measured in terms of the “diversity” of research areas in the references that an article cites. The standard indicators used are borrowed mostly from other research areas, notably from ecology (biodiversity measures) and economics (concentration measures). This paper argues that while the measures used in biodiversity research have evolved over time, the interdisciplinarity indicators used in bibliometrics can be mapped to a subset of biodiversity measures from the first and second generations. We discuss the third generation of biodiversity measures and especially the Leinster–Cobbold diversity indices (LCDiv) (Leinster and Cobbold in Ecology 93(3):477–489, 2012). We present a case study based on a previously published dataset of interdisciplinarity study in the field of bio-nano science (Rafols and Meyer in Scientometrics 82(2):263–287, 2010). We replicate the findings of this study to show that the various interdisciplinarity measures are in fact special cases of the LCDiv. The paper discusses some interesting properties of the LCDiv which make them more appealing in the study of disciplinary diversity than the standard interdisciplinary diversity indicators.},
-author = {Mugabushaka, Alexis-Michel and Kyriakou, Anthi and Papazoglou, Theo},
-doi = {10.1007/s11192-016-1865-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mugabushaka, Kyriakou, Papazoglou - 2016 - Bibliometric indicators of interdisciplinarity the potential of the Leinster–Cobbold diversit.pdf:pdf},
-journal = {Scientometrics},
-number = {2},
-pages = {593--607},
-title = {{Bibliometric indicators of interdisciplinarity: the potential of the Leinster–Cobbold diversity indices to study disciplinary diversity}},
-url = {http://link.springer.com/10.1007/s11192-016-1865-x},
-volume = {107},
-year = {2016}
-}
-@article{Stoyan2000a,
-abstract = {Ripley's K function, the L function and the pair correlation function are important second order characteristics of spatial point processes. These functions are usually estimated by ratio estimators, where the numerators are Horvitz-Thompson edge corrected estimators and the denominators estimate the intensity or its square, It is possible to improve these estimators with respect to bias and estimation variance by means of adapted distance dependent intensity estimators. Further improvement is possible by means of refined estimators of the square of intensity. All this is shown by statistical analysis of simulated Poisson, cluster and hard core processes.},
-annote = {Article
-English
-SCAND J STATIST
-377VC},
-author = {Stoyan, Dietrich and Stoyan, Helga},
-doi = {10.1111/1467-9469.00213},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan, Stoyan - 2000 - Improving ratio estimators of second order point process characteristics.pdf:pdf},
-journal = {Scandinavian Journal of Statistics},
-number = {4},
-pages = {641--656},
-title = {{Improving ratio estimators of second order point process characteristics}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9469.00213/abstract},
-volume = {27},
-year = {2000}
-}
-@article{Marcon2015,
-abstract = {L'agglom{\'{e}}ration des activit{\'{e}}s {\'{e}}conomiques est ind{\'{e}}niable (Krugman, 1991) et chacun peut ais{\'{e}}ment citer des exemples de quartiers sp{\'{e}}cialis{\'{e}}s au sein des villes ou des clusters d'activit{\'{e}}s par exemple. L'explication des ph{\'{e}}nom{\`{e}}nes d'agglom{\'{e}}ration semble {\^{e}}tre {\`{a}} pr{\'{e}}sent bien appr{\'{e}}hend{\'{e}}e th{\'{e}}oriquement (Fujita et al., 1999 ; Fujita et Thisse, 2002) mais les recherches empiriques ne semblent pas avoir atteint un tel stade de maturit{\'{e}} (Rosenthal et Strange, 2004, Ellison et al., 2010 ; Gibbons et al., 2014). Durant la derni{\`{e}}re d{\'{e}}cennie, de nombreuses recherches en {\'{e}}conomie spatiale ont port{\'{e}} sur les mesures de concentration g{\'{e}}ographique. Les {\'{e}}conomistes retenaient traditionnellement des mesures reposant sur un zonage du territoire (comme l'indice de Gini) mais des travaux r{\'{e}}cents ont montr{\'{e}} que discr{\'{e}}tiser l'espace pouvait engendrer des biais (Briant et al., 2010). L'utilisation de mesures fond{\'{e}}es sur les distances (s{\'{e}}parant les entit{\'{e}}s analys{\'{e}}es) et non sur un zonage est aujourd'hui recommand{\'{e}}e (Combes et al., 2006). Notre contribution m{\'{e}}thodologique montre qu'une attention particuli{\`{e}}re doit encore {\^{e}}tre port{\'{e}}e {\`{a}} la d{\'{e}}finition de la concentration spatiale pour {\'{e}}valuer l'agglom{\'{e}}ration des activit{\'{e}}s {\'{e}}conomiques. {\`{A}} partir de la localisation des commerces de d{\'{e}}tail sur l'aire urbaine de Lyon notamment, nous montrons, en utilisant trois mesures de concentration r{\'{e}}cemment introduites en {\'{e}}conomie spatiale (Kd, D et M), que les r{\'{e}}sultats obtenus ne convergent pas syst{\'{e}}matiquement. Cette diff{\'{e}}rence dans les estimations provient de la d{\'{e}}finition de la concentration spatiale retenue qui peut {\^{e}}tre absolue (pr{\'{e}}sence importante d'activit{\'{e}}s), topographique (densit{\'{e}} {\'{e}}lev{\'{e}}e d'activit{\'{e}}s) ou relative (surrepr{\'{e}}sentation de certaines activit{\'{e}}s). Nous recommandons alors que le choix de la mesure de concentration soit suffisamment motiv{\'{e}} d'un point de vue th{\'{e}}orique pour appr{\'{e}}cier correctement le ph{\'{e}}nom{\`{e}}ne analys{\'{e}} et ainsi apporter une {\'{e}}valuation satisfaisante de la distribution {\'{e}}tudi{\'{e}}e.},
-author = {Marcon, Eric and Puech, Florence},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech - 2015 - Mesures de la concentration spatiale en espace continu th{\'{e}}orie et applications.pdf:pdf},
-journal = {{\'{E}}conomie et Statistique},
-pages = {105--131},
-title = {{Mesures de la concentration spatiale en espace continu : th{\'{e}}orie et applications}},
-url = {https://www.insee.fr/fr/statistiques/fichier/1377634/ES474E.pdf},
-volume = {474},
-year = {2015}
-}
-@incollection{Baddeley2006,
-abstract = {We describe practical techniques for fitting stochastic models to spatial point pattern data in the statistical package R. The techniques have been implemented in our package spatstat in R. They are demonstrated on two example datasets.},
-author = {Baddeley, Adrian J. and Turner, Rolf},
-booktitle = {Case Studies in Spatial Point Process Modeling},
-doi = {10.1007/0-387-31144-0_2},
-editor = {Baddeley, Adrian and Gregori, Pablo and Mateu, Jorge and Stoica, Radu and Stoyan, Dietrich},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, Turner - 2006 - Modelling Spatial Point Patterns in R. Case Studies in Spatial Point Process Modeling.pdf:pdf},
-isbn = {978-0-387-31144-9},
-pages = {23--74},
-publisher = {Springer New York},
-title = {{Modelling Spatial Point Patterns in R}},
-url = {http://dx.doi.org/10.1007/0-387-31144-0{\_}2},
-volume = {185},
-year = {2006}
-}
-@incollection{Baldwin2004,
-address = {Amsterdam},
-author = {Baldwin, Richard E. and Martin, Philippe},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baldwin, Martin - 2004 - Agglomeration and regional growth.pdf:pdf},
-publisher = {Elsevier. North Holland},
-title = {{Agglomeration and regional growth}},
-url = {http://www.hec.unil.ch/deep/evenements/3c-combes1.pdf},
-year = {2004}
-}
-@article{Dutilleul1993,
-abstract = {Experimental design should be accommodated to spatial heterogeneity in nature as well as indoors, whether it is a nuisance or a characteristic of interest, combined or not with assessment of treatment effects. The following analysis-of-variance approach to quantification of spatial heterogeneity is based on the adequate design of ecological field experiments, according to the type and the scale of heterogeneity of concern (at small scale, patches, one- or two-dimensional gradients). There are no recipes for doing so and judgment must be exercised every time; the experimenter's knowledge about the experimental material, combined with premanipulation or control, then, provides a useful prerequisite. For patches and environmental gradients, in the presence of treatment assignment, recommended designs require the blocking principle ofgrouping similar experimental units, which allows avoidance of spurious treatment effects and inflated error mean square. Completely randomized designs should only be used in the very particular case of spatial homogeneity at large scale. Illustrations in ecological field experimentation are given and discussed.},
-author = {Dutilleul, Pierre},
-doi = {10.2307/1939923},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dutilleul - 1993 - Spatial Heterogeneity and the Design of Ecological Field Experiments(2).pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1646--1658},
-title = {{Spatial Heterogeneity and the Design of Ecological Field Experiments}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1939923/abstract},
-volume = {74},
-year = {1993}
-}
-@article{Golestani2013,
-abstract = {Species abundance distribution ( SAD) is one of the important measures of biodiversity and one of the most significant concepts in ecology communities. Using this concept, the biologists can infer a lot of information from their collected data. In this article, we proposed a new method for predicting SAD. This method is based on the combination of several measures parameterized by machine learning techniques and decomposition of the model in sub-ranges having their proper combination. The goal is to use the combination of several individual models to design a better and more informative model. We show in this article by using many datasets representing different ecological situations that our new method is more robust and outperforms the predictive capacity of the other existing models.},
-annote = {ISI Document Delivery No.: 285ZG
-Times Cited: 0
-Cited Reference Count: 39
-Golestani, Abbas Gras, Robin
-Walter de gruyter gmbh
-Berlin},
-author = {Golestani, A. and Gras, R.},
-doi = {10.1515/ijb-2012-0033},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Golestani, Gras - 2013 - A New Species Abundance Distribution Model Based on Model Combination.pdf:pdf},
-journal = {International Journal of Biostatistics},
-number = {1},
-pages = {33--48},
-title = {{A New Species Abundance Distribution Model Based on Model Combination}},
-volume = {9},
-year = {2013}
-}
-@book{Pielou1969,
-abstract = {This book covers population dynamics, spatial patterns in 1-species populations, spatial relations of 2 or more species and of many-species populations.},
-address = {New York},
-author = {Pielou, Evelyn C.},
-publisher = {Wiley},
-title = {{An Introduction to Mathematical Ecology}},
-year = {1969}
-}
-@book{MacArthur1967,
-author = {MacArthur, R.H and Wilson, E.O},
-booktitle = {Monographs in Population Biology},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/MacArthur, Wilson - 1967 - The theory of island biogeography.pdf:pdf},
-isbn = {069108050X},
-publisher = {Princeton University Press},
-title = {{The Theory of Island Biogeography}},
-volume = {1},
-year = {1967}
-}
-@article{Bentley2015,
-abstract = {William Bunge's Fitzgerald: Portrait of a Revolution, initially published in 1971, is an enthralling verbal and visual account of the historical and geographical development of a one-square-mile neighborhood in Detroit. The original analysis of the Fitzgerald neighborhood was based on intensive field-based research conducted in a theoretical context of race and racism. The research reported here maintains that context but updates Fitzgerald's account of the neighborhood's built environment through a spatial analysis that uses parcel-by-parcel data generated in Google Earth and Google Street View instead of data collected in the field. Current spatial patterns of deterioration in the built environment are similar to those described in Fitzgerald, but positive sites are also apparent and often colocated with negative ones.},
-author = {Bentley, George C. and McCutcheon, Priscilla and Cromley, Robert G. and Hanink, Dean M.},
-doi = {10.1080/00330124.2015.1102027},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bentley et al. - 2015 - Fitzgerald A Return to the Neighborhood and Its Contemporary Structural and Geographical Contexts.pdf:pdf},
-journal = {The Professional Geographer},
-number = {3},
-pages = {414--426},
-title = {{Fitzgerald: A Return to the Neighborhood and Its Contemporary Structural and Geographical Contexts}},
-url = {http://www.tandfonline.com/doi/full/10.1080/00330124.2015.1102027},
-volume = {68},
-year = {2015}
-}
-@article{He1996,
-abstract = {The diversity of trees (species richness, abundance and Shannon diversity) in a tropical rain forest in the Pasoh Reserve, Peninsular Malaysia, was studied from the viewpoint of its spatial organization in order to formulate hypotheses about the origin of the observed spatial patterns - specifically to determine whether tropical forest communities are in a state of equilibrium or non-equilibrium. Three aspects were examined. First, changes in diversity were studied with respect to sampling area and sampling designs. This showed that a minimum area of 5-10 ha is recommended by the species-area curves, while 2-5 ha seem appropriate based on the Shannon diversity- area curves. Different sampling designs significantly affect the species-area curves. The power function, which can be derived under the equilibrium assumption, is not appropriate to fit the observed diversity-area curves. Secondly, the spatial features of diversity variables were studied. Variograms showed that there are dominant short-range effects (around 150 m), obvious anisotropic distribution, and high random variation in the diversity data. Thirdly, a study in which the variation of the diversity measures was partitioned into environmental (topographic) and spatial components indicated that the spatial organisation of that community is mostly unpredictable. It is concluded that there may be many processes controlling the formation of the spatial patterns in tropical rain forest, but that unidentified causes, affecting mainly the small-scale processes ({\textless}20 m), seem responsible for the large amount of undetermined variation in the diversity data sets. The study suggests that the Pasoh forest may not be in a state of equilibrium.},
-author = {He, FangLiang and Legendre, Pierre and Lafrankie, James V.},
-doi = {10.1046/j.1365-2699.1996.00976.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/He, Legendre, Lafrankie - 1996 - Spatial pattern of diversity in a tropical rain forest in Malaysia.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {1},
-pages = {57--74},
-title = {{Spatial pattern of diversity in a tropical rain forest in Malaysia}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2699.1996.00976.x/abstract{\#}},
-volume = {23},
-year = {1996}
-}
-@article{Cardoso2014a,
-abstract = {Complete sampling of all dimensions of biodiversity is a formidable task, even for small areas. Undersampling is the norm, and the underquantification of diversity is a common outcome. Estimators of taxon diversity (TD) are widely used to correct for undersampling. Yet, no similar strategy has been developed for phylogenetic (PD) or functional (FD) diversity. We propose three ways of estimating PD and FD, building on estimators originally developed for TD: (i) correcting PD and FD values based on the completeness of TD; (ii) fitting asymptotic functions to accumulation curves of PD and FD; and (iii) adapting nonparametric estimators to PD and FD data. Using trees as a common framework for the estimation of PD and FD, we tested the approach with European mammal and Azores Islands arthropod data. We demonstrated that different methods were able to considerably reduce the undersampling bias and often correctly estimated true diversity using a fraction of the samples necessary to reach complete sampling. Besides the utility of knowing the true diversity of an assemblage from incomplete samples, the use of estimators may present further advantages. For instance, comparisons between sites or time periods are possible only if either sampling is complete or sampling effort is equivalent and sufficient to allow sensible comparisons. Also, as PD and FD asymptote faster than TD, comparisons between these different dimensions may require unbiased values. The framework now proposed combines taxon, phylogenetic and functional diversity into a single framework, offering a tool for future developments involving these different facets of biological diversity.},
-author = {Cardoso, Pedro and Rigal, Fran{\c{c}}ois and Borges, Paulo a. V. and Carvalho, Jos{\'{e}} C.},
-doi = {10.1111/2041-210X.12173},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cardoso et al. - 2014 - A new frontier in biodiversity inventory a proposal for estimators of phylogenetic and functional diversity.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {5},
-pages = {452--461},
-title = {{A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12173},
-volume = {5},
-year = {2014}
-}
-@article{Rajaram2017,
-abstract = {From economic inequality and species diversity to power laws and the analysis of multiple trends and trajectories, diversity within systems is a major issue for science. Part of the challenge is measuring it. Shannon entropy H has been used to re-think diversity within probability distributions, based on the notion of information. However, there are two major limitations to Shannon's approach. First, it cannot be used to compare diversity distributions that have different levels of scale. Second, it cannot be used to compare parts of diversity distributions to the whole. To address these limitations, we introduce a re-normalization of probability distributions based on the notion of case-based entropy Cc as a function of the cumulative probability c. Given a probability density p(x), Cc measures the diversity of the distribution up to a cumulative probability of c, by computing the length or support of an equivalent uniform distribution that has the same Shannon information as the conditional distribution of pc(x) up to cumulative probability c. We illustrate the utility of our approach by re-normalizing and comparing three well-known energy distributions in physics, namely, the Maxwell-Boltzmann, Bose-Einstein and Fermi- Dirac distributions for energy of sub-atomic particles. The comparison shows that Cc is a vast improvement overH as it provides a scale-free comparison of these diversity distributions and also allows for a comparison between parts of these diversity distributions.},
-author = {Rajaram, R. and Castellani, B. and Wilson, A. N.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rajaram, Castellani, Wilson - 2017 - Advancing Shannon Entropy for Measuring Diversity in Systems.pdf:pdf},
-journal = {Complexity},
-title = {{Advancing Shannon Entropy for Measuring Diversity in Systems}},
-url = {https://www.hindawi.com/journals/complexity/aip/8715605/},
-volume = {in press},
-year = {2017}
-}
-@article{Brose2003,
-abstract = {The number of species in an area is critical to the development of evolutionary and ecological theory from mass extinctions to island biogeography. Still, the factors influencing the accuracy of estimators of species richness are poorly understood. We explored these factors by simulating landscapes, that varied in species richness, relative abundances, and the spatial distribution. We compared the extrapolations of nine nonparametric estimators and two species accumulation curves under three sampling intensities. Community evenness of species' abundances, sampling intensity, and the level of true species richness significantly influenced bias, precision, and accuracy of the estimations. Perhaps most surprisingly, the effects of gradient strength and spatial autocorrelation type were generally insignificant. The nonparametric estimators were substantially less biased and more precise than the species accumulation curves. Observed species richness was most biased. Community evenness, sampling intensity, and the level of true species richness influenced the performance of the nonparametric estimators indirectly via the fraction of all species found in a sample or "sample coverage." For each particular level of sample coverage, a single estimator was most accurate. Choice of estimator is confounded by a priori uncertainty about the sample coverage. Accordingly, researchers can extrapolate species richness by various estimators and base the estimator choice on the mean estimated sample coverage. Alternatively, the most reliable estimator with respect to community evenness can be chosen. These predictions from our simulations are confirmed in two field studies.},
-author = {Brose, Ulrich and Martinez, Neo D. and Williams, Richard J.},
-doi = {10.1890/02-0558},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brose, Martinez, Williams - 2003 - Estimating species richness Sensitivity to sample coverage and insensitivity to spatial patterns.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2364--2377},
-title = {{Estimating species richness: Sensitivity to sample coverage and insensitivity to spatial patterns}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/02-0558/abstract},
-volume = {84},
-year = {2003}
-}
-@article{Tucker2013,
-abstract = {Aim Biogeographical theory and conservation valuation schemes necessarily involve assessing how biodiversity is distributed through space and biodiversity' encapsulates many different aspects of biological organization and information. While biogeography may try to explain biodiversity patterns, successful conservation strategies should attempt to maximize different aspects of diversity. Ultimately, diversity patterns are the product of evolutionary history, and research and conservation efforts seek to understand the unequal distribution of evolutionary history. For conservation efforts, results have been inconsistent as to whether species richness (SR) provides sufficient surrogacy for evolutionary history. Here, we provide a conceptual framework allowing for the direct comparison of taxonomic richness and phylogenetic diversity (PD), both in terms of their mechanistic relationship and the relationship between their spatial distributions. Location Global. Methods We present a framework that relates regional SR, PD, biogeographically weighted evolutionary distinctiveness and biogeographically weighted SR. Further, we use simulations to illustrate how the size of the species pool, topological patterns within the phylogeny and autocorrelation in spatial distributions affect the correlation among metrics. Results In regions that include both recently diversified groups and ancient species poor lineages, large species pools and low spatial autocorrelation, the correlation between biodiversity measures is lower than regions with low richness, balanced phylogenetic trees and high spatial autocorrelation. Main conclusions We can now understand and predict when regional richness and PD should be strongly correlated. This congruency is the product of evolutionary and ecological processes that determine species pool membership and community assembly. Further, in regions where SR is not expected to be congruent with phylogenetic distinctiveness, re-examining how existing reserve networks protect the multiple aspects of biodiversity is critically important.},
-annote = {ISI Document Delivery No.: 163HU
-Times Cited: 0
-Cited Reference Count: 59
-Tucker, Caroline M. Cadotte, Marc W.
-NSERC CGS-D; NSERC [386151]; Canada Foundation for Innovation; Ontario Research Fund
-We wish to thank T. J. Davies for numerous discussions about phylogeny and conservation and for guidance on manipulating phylogenetic topologies. We also wish to thank Dave Richardson and Mathieu Rouget and two anonymous referees for helping to improve this manuscript. C.M.T. is supported by an NSERC CGS-D scholarship. MWC is generously supported by an NSERC discovery grant ({\#}386151) and funding from the Canada Foundation for Innovation and Ontario Research Fund.
-Wiley-blackwell
-Hoboken},
-author = {Tucker, Caroline M. and Cadotte, Marc W.},
-doi = {10.1111/ddi.12087},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tucker, Cadotte - 2013 - Unifying measures of biodiversity understanding when richness and phylogenetic diversity should be congruent.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {7},
-pages = {845--854},
-title = {{Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12087/full},
-volume = {19},
-year = {2013}
-}
-@article{Catin1991,
-abstract = {Analyse de l'impact des {\'{e}}conomies d'agglom{\'{e}}ration sur les gains de productivit{\'{e}} industrielle dans les r{\'{e}}gions fran{\c{c}}aises, {\`{a}} l'aide d'un mod{\`{e}}le g{\'{e}}n{\'{e}}ralis{\'{e}} de Kaldor-Verdoorn d{\'{e}}riv{\'{e}} d'une fonction de production CES. Les {\'{e}}conomies d'urbanisation et de localisation jouent de mani{\`{e}}re tr{\`{e}}s diff{\'{e}}rente sur les rendements d'{\'{e}}chelle et les gains de productivit{\'{e}} autonome. Les relations conduisent {\`{a}} examiner et {\`{a}} approfondir le r{\^{o}}le des structures spatiales dans la dynamique industrielle.},
-author = {Catin, Maurice},
-journal = {Revue d'Economie R{\'{e}}gionale et Urbaine},
-pages = {565--598},
-title = {{Economies d'agglom{\'{e}}ration et gains de productivit{\'{e}}}},
-url = {http://geoprodig.cnrs.fr/items/show/62127},
-volume = {5},
-year = {1991}
-}
-@article{Browak2000,
-abstract = {Studies that are unprecedented in scale, detail or approach show that niche partitioning contributes less, and chance events more, than expected to maintaining tree species richness via gap dynamics in tropical and temperate forests. Some tree species are differentially adapted for regeneration in different gap microenvironments. However, the stochastic availability of gaps, and limited recruitment of juveniles, mean that gaps are filled mostly by chance occupants rather than by best adapted species. This chance survival can slow competitive exclusion and maintain tree diversity. Gap dynamics do not explain the latitudinal gradient in tree richness.},
-author = {Browak, Nicholas and Busing, Richard T.},
-doi = {10.1016/S0169-5347(00)01822-X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Browak, Busing - 2000 - Niche versus chance and tree diversity in forest gaps.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {5},
-pages = {183--188},
-title = {{Niche versus chance and tree diversity in forest gaps}},
-url = {http://www.cell.com/trends/ecology-evolution/references/S0169-5347{\%}2800{\%}2901822-X},
-volume = {15},
-year = {2000}
-}
-@article{Cadotte2013,
-abstract = {Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait-based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait-phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.},
-author = {Cadotte, Marc and Albert, Cecile H. and Walker, Steve C.},
-doi = {10.1111/ele.12161},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte, Albert, Walker - 2013 - The ecology of differences Assessing community assembly with trait and evolutionary distances.pdf:pdf},
-journal = {Ecology Letters},
-number = {10},
-pages = {1234--1244},
-title = {{The ecology of differences: Assessing community assembly with trait and evolutionary distances}},
-volume = {16},
-year = {2013}
-}
-@article{Roggy1999b,
-abstract = {The suitability of the natural 15N abundance and of total N concentration of leaves as indicators of the type of plant N nutrition in a rain forest of French Guiana were tested. Leaf samples from primary legume species, non-legumes (pioneer species) and from the non-N₂-fixing species Dicorynia guianensis were analyzed. Both $\delta$ 15N and total leaf N varied widely (-1 ≤ $\delta$ 15N (‰) ≤ 7 and 1 ≤ leaf N({\%}) ≤ 3.2) suggesting possible distinctions between diazotrophic and non-fixing plants. The $\delta$ 15N also revealed two statistically distinct groups of non-N₂-fixing species ($\delta$ 15N = 5.14 ± 0.3 vs $\delta$ 15N = 1.65 ± 0.17) related to the different ecological behaviors of these species in the successional processes. We conclude that the $\delta$ 15N signature of plant leaves combined with their total N concentration may be relevant indicators for identifying functional groups within the community of non-N₂-fixing species, as well as for detecting diazotrophy. Despite the variability in the $\delta$ 15N of the non-N₂-fixing species, N₂-fixing groups can still be identified, provided that plants are simultaneously classified taxonomically, by their leaf $\delta$ 15N and total N concentration and by the presence or absence of nodules. The variability in the $\delta$ 15N of the non-fixing species is discussed.},
-author = {Roggy, Jean-Christophe and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise and Gourbiere, F. and Casabianca, H. and Garbaye, Jean and Domenach, Anne-Marie},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roggy et al. - 1999 - Leaf natural 15N abundance and total N concentration as potential indicators of plant N nutrition in legumes and p.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {171--182},
-title = {{Leaf natural 15N abundance and total N concentration as potential indicators of plant N nutrition in legumes and pioneer species in a rain forest of French Guiana}},
-url = {http://www.jstor.org/stable/4222374},
-volume = {120},
-year = {1999}
-}
-@article{Gregorius2009a,
-abstract = {Understanding the significance of the distribution of genetic or phenotypic variation over populations is one of the central concerns of population genetic and ecological research. The import of the research decisively depends on the measures that are applied to assess the amount of variation residing within and between populations. Common approaches can be classified under two perspectives: differentiation and apportionment. While the former focuses on differences (distances) in trait distribution between populations, the latter considers the division of the overall trait variation among populations. Particularly when multiple populations are studied, the apportionment perspective is usually given preference (via F(ST)/G(ST) indices), even though the other perspective is also relevant. The differences between the two perspectives as well as their joint conceptual basis can be exposed by referring them to the association between trait states and population affiliations. It is demonstrated that the two directions, association of population affiliation with trait state and of trait state with population affiliation, reflect the differentiation and the apportionment perspective, respectively. When combining both perspectives and applying the suggested measure of association, new and efficient methods of analysis result, as is outlined for population genetic processes. In conclusion, the association approach to an analysis of the distribution of trait variation over populations resolves problems that are frequently encountered with the apportionment perspective and its commonly applied measures in both population genetics and ecology, suggesting new and more comprehensive methods of analysis that include patterns of differentiation and apportionment.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.1007/s12064-009-0064-1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 2009 - Distribution of variation over populations.pdf:pdf},
-journal = {Theory in Biosciences},
-number = {3},
-pages = {179--89},
-title = {{Distribution of variation over populations}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2766040{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {128},
-year = {2009}
-}
-@article{Petchey2004a,
-annote = {Article},
-author = {Petchey, Owen L. and Hector, Andrew and Gaston, Kevin J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Petchey, Hector, Gaston - 2004 - How do different measures of functional diversity perform.pdf:pdf},
-journal = {Ecology},
-keywords = {Petchey (2004b).pdf},
-mendeley-tags = {Petchey (2004b).pdf},
-number = {3},
-pages = {847--857},
-title = {{How do different measures of functional diversity perform?}},
-volume = {85},
-year = {2004}
-}
-@article{Cowell1980,
-abstract = {The analogy between information theory and income distribution analysis is exploited to derive a number of measures of distributional change. These include not only counterparts of the regular entropy measures, but also of the entire, rich "generalised entropy" family. The paper analyses the properties of the measures, and in particular their performance in response to "independent" transfers and to cases where an income transfer in the world distribution automatically produces a corresponding transfer in the new distribution. The relationship of such "functionally dependent" transfers to a measure of tax progression is examined.},
-author = {Cowell, Frank A.},
-doi = {10.1016/0014-2921(80)90051-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cowell - 1980 - Generalized entropy and the measurement of distributional change.pdf:pdf},
-isbn = {0014-2921},
-issn = {00142921},
-journal = {European Economic Review},
-pages = {147--159},
-title = {{Generalized entropy and the measurement of distributional change}},
-volume = {13},
-year = {1980}
-}
-@article{Cannon1998,
-abstract = {The effects of commercial logging on tree diversity in tropical rainforest are largely unknown. In this study, selectively logged tropical rainforest in Indonesian Borneo is shown to contain high tree species richness, despite severe structural damage. Plots logged 8 years before sampling contained fewer species of trees greater than 20 centimeters in diameter than did similar-sized unlogged plots. However, in samples of the same numbers of trees (requiring a 50 percent larger area), logged forest contained as many tree species as unlogged forest. These findings warrant reassessment of the conservation potential of large tracts of commercially logged tropical rainforest.},
-author = {Cannon, Charles H. and Peart, David R. and Leighton, Mark},
-doi = {10.1126/science.281.5381.1366},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cannon, Peart, Leighton - 1998 - Tree Species Diversity in Commercially Logged Bornean Rainforest.pdf:pdf},
-journal = {Science},
-number = {5381},
-pages = {1366--1368},
-title = {{Tree Species Diversity in Commercially Logged Bornean Rainforest}},
-url = {http://science.sciencemag.org/content/281/5381/1366.full},
-volume = {281},
-year = {1998}
-}
-@article{Hurlbert1971,
-abstract = {The recent literature on species diversity contains many semantic, conceptual, and technical problems. It is suggested that, as a result of these problems, species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species-number relations and rely less on information theoretic and other analogies. As multispecific collections of organisms possess numerous statistical properties which conform to the conventional criteria for diversity indices, such collections are not intrinsically arrangeable in linear order along some diversity scale. Several such properties or "species composition parameters" having straightforward biological interpretations are presented as alternatives to the diversity approach. The two most basic of these are simply {\$}\backslashDelta{\_}1= [\backslashfrac{\{}N{\}}{\{}N-1{\}}][{\^{}}1-\backslashSigma{\_}i (\backslashfrac{\{}N{\_}i{\}} {\{}N{\}}){\^{}}2]{\$} =the proportion of potential interindividual encounters which is interspecific (as opposed to intraspecific), assuming every individual in the collection can encounter all other individuals, and {\$}E(S{\_}n)= {\^{}}\backslashSigma{\_}i [1-\backslashfrac{\{}(\backslashbinom{\{}N-N{\_}i{\}}{\{}n{\}}){\}}{\{}(\backslashbinom{\{}N{\}}{\{}n{\}}){\}}]{\$} =the expected number of species in a sample of n individuals selected at random from a collection containing N individuals, S species, and Ni individuals in the ith species.},
-author = {Hurlbert, Stuart H.},
-doi = {10.2307/1934145},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hurlbert - 1971 - The Nonconcept of Species Diversity A Critique and Alternative Parameters.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {577--586},
-title = {{The Nonconcept of Species Diversity: A Critique and Alternative Parameters}},
-url = {http://www.esajournals.org/doi/abs/10.2307/1934145},
-volume = {52},
-year = {1971}
-}
-@article{Slik2015,
-abstract = {The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between {\~{}}40,000 and {\~{}}53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of {\~{}}19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of {\~{}}4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.},
-author = {Slik, J. W. Ferry and Arroyo-Rodr{\'{i}}guez, V{\'{i}}ctor and Aiba, Shin-Ichiro and Alvarez-Loayza, Patricia and Alves, Luciana F. and Ashton, Peter S. and Balvanera, Patricia and Bastian, Meredith L. and Bellingham, Peter J. and van den Berg, Eduardo and Bernacci, Luis and {da Concei{\c{c}}{\~{a}}o Bispo}, Polyanna and Blanc, Lilian and B{\"{o}}hning-Gaese, Katrin and Boeckx, Pascal and Bongers, Frans and Boyle, Brad and Bradford, Matt and Brearley, Francis Q. and {Breuer-Ndoundou Hockemba}, Mireille and Bunyavejchewin, Sarayudh and {Calderado Leal Matos}, Darley and Castillo-Santiago, Miguel and Catharino, Eduardo L. M. and Chai, Shauna-Lee and Chen, Yukai and Colwell, Robert K. and Robin, Chazdon L. and Clark, Connie J. and Clark, David B. and Clark, Deborah A.. and Culmsee, Heike and Damas, Kipiro and Dattaraja, Handanakere S. and Dauby, Gilles and Davidar, Priya and DeWalt, Saara J. and Doucet, Jean-Louis and Duque, Alvaro and Durigan, Giselda and Eichhorn, Karl A. O. and Eisenlohr, Pedro V. and Eler, Eduardo and Ewango, Corneille and Farwig, Nina and Feeley, Kenneth J. and Ferreira, Leandro and Field, Richard and {de Oliveira Filho}, Ary T. and Fletcher, Christine and Forshed, Olle and Franco, Geraldo and Fredriksson, Gabriella and Gillespie, Thomas and Gillet, Jean-Fran{\c{c}}ois and Amarnath, Giriraj and Griffith, Daniel M. and Grogan, James and Gunatilleke, Nimal and Harris, David and Harrison, Rhett and Hector, Andy and Homeier, J{\"{u}}rgen and Imai, Nobuo and Itoh, Akira and Jansen, Patrick A. and Joly, Carlos A. and de Jong, Bernardus H. J. and Kartawinata, Kuswata and Kearsley, Elizabeth and Kelly, Daniel L. and Kenfack, David and Kessler, Michael and Kitayama, Kanehiro and Kooyman, Robert and Larney, Eileen and Laumonier, Yves and Laurance, Susan and Laurance, William F. and Lawes, Michael J. and Amaral, I{\^{e}}da Le{\~{a}}o and Letcher, Susan G. and Lindsell, Jeremy and Lu, Xinghui and Mansor, Asyraf and Marjokorpi, Antti and Martin, Emanuel H. and Meilby, Henrik and Melo, Felipe P. L. and Metcalfe, Daniel J. and Medjibe, Vincent P. and Metzger, Jean Paul and Millet, Jerome and Mohandass, D. and Montero, Juan C. and {de Morisson Valeriano}, M{\'{a}}rcio and Mugerwa, Badru and Nagamasu, Hidetoshi and Nilus, Reuben and Ochoa-Gaona, Susana and Onrizal and Page, Navendu and Parolin, Pia and Parren, Marc and Parthasarathy, Narayanaswamy and Paudel, Ekananda and Permana, Andrea and Piedade, Maria T. F. and Pitman, Nigel C. A. and Poorter, Lourens and Poulsen, Axel D. and Poulsen, John and Powers, Jennifer and Prasad, Rama C. and Puyravaud, Jean-Philippe and Razafimahaimodison, Jean-Claude and Reitsma, Jan and dos Santos, Jo{\~{a}}o Roberto and {Roberto Spironello}, Wilson and Romero-Saltos, Hugo and Rovero, Francesco and Rozak, Andes Hamuraby and Ruokolainen, Kalle and Rutishauser, Ervan and Saiter, Felipe and Saner, Philippe and Santos, Br{\'{a}}ulio A. and Santos, Fernanda and Sarker, Swapan K. and Satdichanh, Manichanh and Schmitt, Christine B. and Sch{\"{o}}ngart, Jochen and Schulze, Mark and Suganuma, Marcio S. and Sheil, Douglas and {da Silva Pinheiro}, Eduardo and Sist, Plinio and Stevart, Tariq and Sukumar, Raman and Sun, I-Fang and Sunderland, Terry and Suresh, H. S. and Suzuki, Eizi and Tabarelli, Marcelo and Tang, Jangwei and Targhetta, Nat{\'{a}}lia and Theilade, Ida and Thomas, Duncan W. and Tchouto, Peguy and Hurtado, Johanna and Valencia, Renato and van Valkenburg, Johan L. C. H. and {Van Do}, Tran and Vasquez, Rodolfo and Verbeeck, Hans and Adekunle, Victor and Vieira, Simone A. and Webb, Campbell O. and Whitfeld, Timothy and Wich, Serge A. and Williams, John and Wittmann, Florian and W{\"{o}}ll, Hannsjoerg and Yang, Xiaobo and {Adou Yao}, C. Yves and Yap, Sandra L. and Yoneda, Tsuyoshi and Zahawi, Rakan A. and Zakaria, Rahmad and Zang, Runguo and de Assis, Rafael L. and {Garcia Luize}, Bruno and Venticinque, Eduardo M.},
-doi = {10.1073/pnas.1423147112},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Slik et al. - 2015 - An estimate of the number of tropical tree species.pdf:pdf},
-journal = {Proceedings of the National Academy of Sciences of the United States of America},
-number = {24},
-pages = {7472--7477},
-title = {{An estimate of the number of tropical tree species}},
-url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1423147112},
-volume = {112},
-year = {2015}
-}
-@article{Pavoine2015a,
-abstract = {Many recent studies have searched to integrate species' functions and phylogenies in the measurement of biodiversity. To obtain easily interpretable measures, some researchers recommended diversity indices expressed in terms of equivalent numbers of species: the number of equally likely and maximally dissimilar species needed to produce the given value of diversity. Then, biodiversity is often calculated at three scales: within communities ($\alpha$ diversity), among communities ($\beta$ diversity) and in a region ($\gamma$ diversity). These three scales are, however, insufficient to tackle the organization of biodiversity in space because, for most organisms, there is a nested hierarchy of multiple scales characterized by different patterns and processes, from the small neighbourhood to the biosphere. We developed methodologies for analysing species, functional, taxonomic or phylogenetic diversity in a hierarchy of multiple scales using equivalent numbers of species. As an example, we analysed the taxonomic and functional diversity of macroinvertebrate assemblages in the Loire River, France, at four levels: within sites ($\alpha$ diversity), among sites within geological regions ($\beta$1 diversity), among geological regions ($\beta$2 diversity) and at the river scale ($\gamma$ diversity). The new hierarchical approaches of biodiversity revealed very low differences among sites within regions and among regions in terms of taxonomy and functional traits (size and diet), despite moderate, significant species turnover among geological regions. We compare our framework with those other authors have developed. We argue that different definitions of $\alpha$, $\beta$, $\gamma$ diversities are used in the literature reflecting different points of view on biodiversity. We make recommendations on how to normalize functional (or phylogenetic) dissimilarities among species to render sites and regions comparable, and discuss the pros and cons of our approach. The hierarchical approaches of biodiversity in terms of ‘equivalent numbers' respond to current demands to obtain intuitive, easily interpretable components of biodiversity. The approaches we propose go beyond current developments by considering a hierarchy of spatial scales and unbalanced sampling design. They will provide powerful tools to detect the ecological and evolutionary processes that act differently at different scales.},
-author = {Pavoine, Sandrine and Marcon, Eric and Ricotta, Carlo},
-doi = {10.1111/2041-210X.12591},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Marcon, Ricotta - 2016 - ‘Equivalent numbers' for species, phylogenetic or functional diversity in a nested hierarchy of multip.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {10},
-pages = {1152--1163},
-title = {{‘Equivalent numbers' for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12591/abstract},
-volume = {7},
-year = {2016}
-}
-@article{Nicotra1998,
-abstract = {Populations of dioecious plant species often exhibit biased sex ratios. Such biases may arise as a result of sex-based differences in life history traits, or as a result of spatial segregation of the sexes. Of these, sex-based differentiation in life history traits is likely to be the most common cause of bias. In dioecious species, selection can act upon the sexes in a somewhat independent way, leading to differentiation and evolution toward sex-specific ecological optima. I examined sex ratio variation and spatial distribution of the tropical dioecious shrub Siparuma grandiflora to determine whether populations exhibited a biased sex ratio, and if so, whether the bias could be explained in terms of nonrandom spatial distribution or sex-based differentiation in life history traits. Sex ratio bias was tested using contingency tables, a logistic regression approach was utilized to examine variation in life history traits, and spatial distributions were analyzed using Ripley's K, a second-order neighborhood analysis. I found that although populations of S. grandiflora have a male-biased sex ratio within and among years, there was no evidence of spatial segregation of the sexes. Rather, the sex ratio bias was shown to result primarily from sex-based differentiation in life history traits; males reproduce at a smaller size and more frequently than females. The sexes also differ in the relationship between plant size and reproductive frequency. Light availability was shown to affect reproductive activity in both sexes, though among infrequently flowering plants, females require higher light levels than males to flower. The results of this study demonstrate that ecologically significant sex-based differentiation has evolved in S. grandiflora.},
-annote = {Article
-English
-OECOLOGIA
-ZW572},
-author = {Nicotra, Adrienne B.},
-doi = {10.1007/s004420050496.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nicotra - 1998 - Sex ratio variation and spatial distribution of Siparuna grandiflora, a tropical dioecious shrub.pdf:pdf},
-journal = {Oecologia},
-number = {1-2},
-pages = {102--113},
-title = {{Sex ratio variation and spatial distribution of Siparuna grandiflora, a tropical dioecious shrub}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs004420050496},
-volume = {115},
-year = {1998}
-}
-@article{Fierer2011,
-abstract = {The elevational gradient in plant and animal diversity is one of the most widely documented patterns in ecology and, although no consensus explanation exists, many hypotheses have been proposed over the past century to explain these patterns. Historically, research on elevational diversity gradients has focused almost exclusively on plant and animal taxa. As a result, we do not know whether microbes exhibit elevational gradients in diversity that parallel those observed for macroscopic taxa. This represents a key knowledge gap in ecology, especially given the ubiquity, abundance, and functional importance of microbes. Here we show that, across a montane elevational gradient in eastern Peru, bacteria living in three distinct habitats (organic soil, mineral soil, and leaf surfaces) exhibit no significant elevational gradient in diversity (r2{\textless}0.17, P{\textgreater}0.1 in all cases), in direct contrast to the significant diversity changes observed for plant and animal taxa across the same montane gradient (r2{\textgreater}0.75, P{\textless}0.001 in all cases). This finding suggests that the biogeographical patterns exhibited by bacteria are fundamentally different from those of plants and animals, highlighting the need for the development of more inclusive concepts and theories in biogeography to explain these disparities.},
-author = {Fierer, Noah and Mccain, Christy M. and Meir, Patrick and Zimmermann, Michael and Rapp, Joshua M. and Silman, Miles R. and Knight, Rob},
-doi = {10.1890/10-1170.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Fierer et al. - 2011 - Microbes do not follow the elevational diversity patterns of plants and animals.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {797--804},
-title = {{Microbes do not follow the elevational diversity patterns of plants and animals}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/10-1170.1/abstract},
-volume = {92},
-year = {2011}
-}
-@article{Allen2009,
-abstract = {Protecting biodiversity involves preserving the maximum number and abundance of species while giving special attention to species with unique genetic or morphological characteristics. In balancing different priorities, conservation policymakers may consider quantitative measures that compare diversity across ecological communities. To serve this purpose, a measure should increase or decrease with changes in community composition in a way that reflects what is valued, including species richness, evenness, and distinctness. However, counterintuitively, studies have shown that established indices, including those that emphasize average interspecies phylogenetic distance, may increase with the elimination of species. We introduce a new diversity index, the phylogenetic entropy, which generalizes in a natural way the Shannon index to incorporate species relatedness. Phylogenetic entropy favors communities in which highly distinct species are more abundant, but it does not advocate decreasing any species proportion below a community structure dependent threshold. We contrast the behavior of multiple indices on a community of phyllostomid bats in the Selva Lacandona. The optimal genus distribution for phylogenetic entropy populates all genera in a linear relationship to their total phylogenetic distance to other genera. Two other indices favor eliminating 12 out of the 23 genera.},
-annote = {ISI Document Delivery No.: 464UG
-Times Cited: 9
-Cited Reference Count: 31
-Allen, Benjamin Kon, Mark Bar-Yam, Yaneer
-UNIV CHICAGO PRESS},
-author = {Allen, Benjamin and Kon, Mark and Bar-Yam, Yaneer},
-doi = {10.1086/600101},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Allen, Kon, Bar-Yam - 2009 - A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bat.pdf:pdf},
-journal = {American Naturalist},
-number = {2},
-pages = {236--243},
-title = {{A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats}},
-volume = {174},
-year = {2009}
-}
-@article{Boersma2016,
-abstract = {Functional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions (“trait space”) and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis-driven approach will increase the rigor and transparency of applied functional trait studies.},
-author = {Boersma, Kate S. and Dee, Laura E. and Miller, Steve J. and Bogan, Michael T. and Lytle, David A. and Gitelman, Alix I.},
-doi = {10.1890/15-0688},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Boersma et al. - 2016 - Linking multidimensional functional diversity to quantitative methods a graphical hypothesis-evaluation framewor.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {583--593},
-title = {{Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis-evaluation framework}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/15-0688/abstract},
-volume = {97},
-year = {2016}
-}
-@article{Sweeney2015,
-abstract = {The objective of this paper is to assess an approach to statistical modeling of point referenced establishment data that permit inclusion of “environmental” or establishment-specific covariates and specific forms of interestablishment interaction. Gibbs models are used to decompose the conditional intensity of the spatial point process into trend and interaction components. The trend is composed of access measures (primarily different classes of roads) and three different interaction processes are tested: Geyer, area interaction, and Strauss hard core. While the models used have proved to be useful in ecology, we are unaware of any applications to establishment or firm data. In empirical application, the models yield intuitively appealing results for the trend component, and the ability to specify the interaction component gives deeper insights into interestablishment spatial dynamics than any previously published methods.},
-author = {Sweeney, Stuart and G{\'{o}}mez-Antonio, Miguel},
-doi = {10.1111/jors.12238},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sweeney, G{\'{o}}mez-Antonio - 2015 - Localization and Industry Clustering Econometrics an Assessment of Gibbs Models for Spatial Point Proces.pdf:pdf},
-journal = {Journal of Regional Science},
-number = {2},
-pages = {257--287},
-title = {{Localization and Industry Clustering Econometrics: an Assessment of Gibbs Models for Spatial Point Processes}},
-url = {http://doi.wiley.com/10.1111/jors.12238},
-volume = {56},
-year = {2015}
-}
-@incollection{Moretti2004,
-address = {Amsterdam},
-author = {Moretti, Enrico},
-booktitle = {Handbook of Urban and Regional Economics},
-editor = {Henderson, J Vernon and Thisse, Jacques-Fran{\c{c}}ois},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moretti - 2004 - Human capital externalities in cities.pdf:pdf},
-publisher = {Elsevier. North Holland},
-title = {{Human capital externalities in cities}},
-year = {2004}
-}
-@article{Sherwin2010,
-abstract = {This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon's entropy-based diversity is the standard for ecological communities. The exponentials of Shannon's and the related "mutual information" excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment. {\textcopyright} 2010.},
-annote = {Cited By (since 1996): 7
-Export Date: 19 October 2012
-Source: Scopus
-Language of Original Document: English
-Correspondence Address: Sherwin, W.B.; Evolution and Ecology Research Centre, School of Biological Earth and Environmental Science, University of New South Wales, Sydney, NSW 2052, Australia; email: W.Sherwin@unsw.edu.au},
-author = {Sherwin, W. B.},
-doi = {10.3390/e12071765},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sherwin - 2010 - Entropy and information approaches to genetic diversity and its expression Genomic geography.pdf:pdf},
-journal = {Entropy},
-number = {7},
-pages = {1765--1798},
-title = {{Entropy and information approaches to genetic diversity and its expression: Genomic geography}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77956415338{\&}partnerID=40{\&}md5=a7bcc5fd660d0b7ada094832d50000aa},
-volume = {12},
-year = {2010}
-}
-@article{Hardin1960,
-abstract = {Opens with a discussion of a meeting of the British Ecological Society devoted to the ecology of closely allied species. Quotes from a contemporary report: 'Discussion centered about Gause's contention that two species with similar ecology cannot live together in the same place... A distinct cleavage of opinion revealed itself on the question of the validity of Gause's concept. Of the main speakers, Mr. Lack, Mr. Elton and Dr. Varley supported the postulate ... Capt. Diver made a vigorous attack on Gause's concept, on the grounds that the mathematical and experimental approaches had been dangerously oversiplified ... Pointing out the difficulty of defining 'similar ecology' he gave examples of many congruent species of both plants and animals apparently living and feeding together.'},
-author = {Hardin, G.},
-doi = {10.1126/science.131.3409.1292},
-isbn = {1333450391},
-issn = {0036-8075},
-journal = {Science},
-number = {3409},
-pages = {1292--1297},
-pmid = {14399717},
-title = {{The Competitive Exclusion Principle}},
-url = {http://www.sciencemag.org/cgi/doi/10.1126/science.131.3409.1292},
-volume = {131},
-year = {1960}
-}
-@article{Bartlett1978,
-abstract = {The method of adjusting plot values by covariance on neighbouring plots in randomized field experiments, suggested by Papadakis in 1937, is re-examined theoretically for both one-dimensional and two-dimensional layouts, making use of Markovian and autonormal models. The gain in efficiency over orthodox randomized block analysis can be appreciable when the number of treatments is fairly large, and can be increased by iterating the analysis ; this also reduces the discrepancy between the apparent accuracy from the residual sum of squares, and the true accuracy of the treatment comparisons after adjustment. Some illustrative examples are included.},
-author = {Bartlett, M. S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bartlett - 1978 - Nearest Neighbour Models in the Analysis of Field Experiments.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {147--174},
-title = {{Nearest Neighbour Models in the Analysis of Field Experiments}},
-url = {http://www.jstor.org/stable/2984750},
-volume = {40},
-year = {1978}
-}
-@article{Gerhold2015,
-abstract = {1. The subdiscipline of 'community phylogenetics' is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co-occurring species within a community is commonly used as a proxy to identify which community assembly pro-cesses may have structured a particular community: phylogenetic clustering as a proxy for abi-otic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition. 2. We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) commu-nities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylo-genetic dispersion is driven predominantly by local and present-day processes. 3. Moreover, technical sophistication of the phylogenetic-patterns-as-proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes. 4. Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macro-evolutionary diversification of habitat lineage-pools (i.e. phylogenetic-patterns-as-result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage-pools and how it affects present-day species coexistence in local communities (i.e. phylogenetic-patterns-as-cause approach). 5. We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage-pool, for example through com-petition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition.},
-author = {Gerhold, Pille and Cahill, James F. and Winter, Marten and Bartish, Igor V. and Prinzing, Andreas},
-doi = {10.1111/1365-2435.12425},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gerhold et al. - 2015 - Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better).pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {600--614},
-title = {{Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)}},
-volume = {29},
-year = {2015}
-}
-@article{Whittaker1960,
-author = {Whittaker, R. H.},
-doi = {10.2307/1943563},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Whittaker - 1960 - Vegetation of the Siskiyou Mountains, Oregon and California.pdf:pdf},
-journal = {Ecological Monographs},
-number = {3},
-pages = {279--338},
-title = {{Vegetation of the Siskiyou Mountains, Oregon and California}},
-url = {https://www.jstor.org/stable/1943563},
-volume = {30},
-year = {1960}
-}
-@article{Gregorius2009,
-abstract = {In biology, the measurement of diversity traditionally focusses on reporting number of unambiguously distinguishable types, thus referring to qualitative (discontinuously varying) traits. Inclusion of frequencies or other weights has produced a large variety of diversity indices. Quantitative (continuously varying) traits do not readily fit into this perspective. In fact, in the context of quantitative traits, the concept of diversity is not always clearly distinguished from the (statistical) notion of dispersion. In many cases the ambiguity even extends to qualitative traits. This is at variance with the broad spectrum of diversity issues ranging, e.g., from ecological and genetic aspects of diversity to functional, structural, systematic, or evolutionary (including phylogenetic) aspects. In view of the urgent need for a more consistent perspective, it is called to attention that all of these aspects, whether of qualitative or quantitative nature, can be gathered under the common roof of binary relations (for qualitative traits two objects are related, for example, if they share the same trait state). A comprehensive concept of (relational) diversity can be developed in two steps: (1) determine the number of unrelated pairs of objects among all admissible pairs as a measure of implicit (relative) diversity, (2) invoke the concept of effective number to transform the implicit measure of diversity into an explicit (absolute) measure. The transformation operates by equating the observed implicit diversity to the implicit diversity obtained for the ideal model of an equivalence relation with classes of equal size. The number of these classes specifies the effective number as an explicit measure of diversity. The wealth of problems that can be treated from this unified perspective is briefly addressed by classifying and interpreting established diversity indices in the light of relational diversity. Desirable applications to the above-mentioned aspects are specified with the help of types of relations such as order, hierarchical, and tree relations. Corresponding biological issues including taxonomic community diversity, mating system, food web, sociological, cladistic and phylogenetic, or hypercycle diversity are suggested for future consideration.},
-author = {Gregorius, Hans-Rolf},
-doi = {10.1016/j.jtbi.2008.11.009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius - 2009 - Relational diversity.pdf:pdf},
-journal = {Journal of theoretical biology},
-number = {1},
-pages = {150--8},
-title = {{Relational diversity}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/19070623},
-volume = {257},
-year = {2009}
-}
-@article{Brown2015,
-abstract = {Spatial statistics are widely used in studies of ecological processes in plant communities, especially to provide evidence of neutral or non-neutral mechanisms that might support species coexistence. The contribution of such statistics has been substantial, but their ability to identify any links between underlying processes and emergent patterns is not certain. We investigate the ability of a number of spatial statistics to distinguish theorized mechanisms of species coexistence (spatial and temporal niche differentiation, neutrality, the Janzen–Connell effect and heteromyopia) in a simulated plant community. We find that individual statistics differ substantially in their sensitivity to these mechanisms, with those based on nearest neighbour species identities being the most sensitive. These differences are largely robust to changes in the strength of the modelled mechanisms when simulated independently and in combination. The spatial signal of niche differentiation is always distinct in simulations that combine mechanisms. Synthesis. We describe full spatial signals of modelled coexistence mechanisms that are observed consistently across statistics and simulated strengths and combinations of mechanisms, and identify a set of spatial statistics that holds particular promise for empirical studies designed to investigate mechanisms of these kinds.},
-author = {Brown, Calum and Illian, Janine B. and Burslem, David F. R. P.},
-doi = {10.1111/1365-2745.12493},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Brown, Illian, Burslem - 2016 - Success of spatial statistics in determining underlying process in simulated plant communities(2).pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {160--172},
-title = {{Success of spatial statistics in determining underlying process in simulated plant communities}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12493},
-volume = {104},
-year = {2016}
-}
-@article{Wright2006d,
-abstract = {Leaf dark respiration (R) is one of the most fundamental physiological processes in plants and is a major component of terrestrial CO2 input to the atmosphere. Still, it is unclear how predictably species vary in R along broad climate gradients. Data for R and other key leaf traits were compiled for 208 woody species from 20 sites around the world. We quantified relationships between R and site climate, and climate-related variation in relationships between R and other leaf traits. Species at higher-irradiance sites had higher mean R at a given leaf N concentration, specific leaf area (SLA), photosynthetic capacity (A(mass)) or leaf lifespan than species at lower-irradiance sites. Species at lower-rainfall sites had higher mean R at a given SLA or A(mass) than species at higher-rainfall sites. On average, estimated field rates of R were higher at warmer sites, while no trend with site temperature was seen when R was adjusted to a standard measurement temperature. Our findings should prove useful for modelling plant nutrient and carbon budgets, and for modelling vegetation shifts with climate change.},
-author = {Wright, Ian J. and Reich, Peter B. and Atkin, O. K. and Lusk, Christopher H. and Tjoelker, Mark G. and Westoby, Mark},
-doi = {10.1111/j.1469-8137.2005.01590.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright et al. - 2006 - Irradiance, temperature and rainfall influence leaf dark respiration in woody plants evidence from comparisons ac.pdf:pdf},
-journal = {New Phytologist},
-number = {2},
-pages = {309--319},
-title = {{Irradiance, temperature and rainfall influence leaf dark respiration in woody plants: evidence from comparisons across 20 sites}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2005.01590.x/full},
-volume = {169},
-year = {2006}
-}
-@article{Faith2006,
-abstract = {A recent paper in this journal (Faith and Baker, 2006) described bio-informatics challenges in the application of the PD (phylogenetic diversity) measure of Faith (1992a), and highlighted the use of the root of the phylogenetic tree, as implied by the original definition of PD. A response paper (Crozier et al. 2006) stated that 1) the (Faith, 1992a) PD definition did not include the use of the root of the tree, and 2) Moritz and Faith (1998) changed the PD definition to include the root. Both characterizations are here refuted. Examples from Faith (1992a,Faith 1992b) document the link from the definition to the use of the root of the overall tree, and a survey of papers over the past 15 years by Faith and colleagues demonstrate that the stated PD definition has remained the same as that in the original 1992 study. PD's estimation of biodiversity at the level of "feature diversity" is seen to have provided the original rationale for the measure's consideration of the root of the phylogenetic tree.},
-author = {Faith, Daniel P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Faith - 2006 - The role of the phylogenetic diversity measure, PD, in bio-informatics getting the definition right.pdf:pdf},
-journal = {Evolutionary Bioinformatics online},
-pages = {277--83},
-title = {{The role of the phylogenetic diversity measure, PD, in bio-informatics: getting the definition right.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2674672{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {2},
-year = {2006}
-}
-@article{Oliver2015,
-abstract = {Accelerating rates of environmental change and the continued loss of global biodiversity threaten functions and services delivered by ecosystems. Much ecosystem monitoring and management is focused on the provision of ecosystem functions and services under current environmental conditions, yet this could lead to inappropriate management guidance and undervaluation of the importance of biodiversity. The maintenance of ecosystem functions and services under substantial predicted future environmental change (i.e., their ‘resilience') is crucial. Here we identify a range of mechanisms underpinning the resilience of ecosystem functions across three ecological scales. Although potentially less important in the short term, biodiversity, encompassing variation from within species to across landscapes, may be crucial for the longer-term resilience of ecosystem functions and the services that they underpin.},
-author = {Oliver, Tom H. and Heard, Matthew S. and Isaac, Nick J.B. and Roy, David B. and Procter, Deborah and Eigenbrod, Felix and Freckleton, Rob and Hector, Andy and Orme, C. David L. and Petchey, Owen L. and Proen{\c{c}}a, V{\^{a}}nia and Raffaelli, David and Suttle, K. Blake and Mace, Georgina M. and Mart{\'{i}}n-L{\'{o}}pez, Berta and Woodcock, Ben A. and Bullock, James M.},
-doi = {10.1016/j.tree.2015.08.009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Oliver et al. - 2015 - Biodiversity and Resilience of Ecosystem Functions.pdf:pdf},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-month = {nov},
-number = {11},
-pages = {673--684},
-title = {{Biodiversity and Resilience of Ecosystem Functions}},
-url = {http://www.sciencedirect.com/science/article/pii/S0169534715002189?via{\%}3Dihub},
-volume = {30},
-year = {2015}
-}
-@unpublished{Lafourcade2003,
-abstract = {Following the model-based approach of Ellison and Glaeser (1997), we develop a framework to test for the link between concentration, spatial clustering and the size of plants. Concentration is an a-spatial concept of variability that can be measured with the standard locational Gini or the more sophisticated Ellison and Glaeser index. By contrast, spatial clustering is directly concerned with distances. Therefore we also use a two-dimensional measure (the Moran index) to identify some speci¯c distance-based patterns. We argue that, in a world where the size of establishments is independent of both concentration and spatial agglomeration, as the standard Dixit-Stiglitz (1977) - Krugman (1980) framework, all the variability in these measures should be accounted for by the variation in the number of plants. Using the Italian 1996 census year data on manufacturing industries, we therefore compare the values and significance of both the EG and Moran indexes computed on an employment and number of plants basis. Our results indicate that, for the majority of Italian manufacturing industries, big plants are much more concentrated than small ones, with size and concentration simultaneously in°uencing each other. On the other hand, small units are shown to be more spatially correlated, suggesting that di{\textregistered}erent externalities may drive (or may be driven by) concentration and agglomeration patterns according to a size-related basis. These results therefore cast some doubt on the relevance of standard monopolistic frameworks to structurally account for the role of the so-called $\backslash$pecuniary" externalities compared to more "localized" ones, such as Marshallian, Jacobian or factor endowments based externalities.},
-author = {Lafourcade, Miren and Mion, Giordano},
-booktitle = {CORE Discussion Paper},
-doi = {10.2139/ssrn.981397},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lafourcade, Mion - 2003 - Concentration, Spatial Clustering and the Size of Plants Disentangling the Sources of Co-location externalitie.pdf:pdf},
-title = {{Concentration, Spatial Clustering and the Size of Plants: Disentangling the Sources of Co-location externalities}},
-url = {https://papers.ssrn.com/soL3/papers.cfm?abstract{\_}id=981397},
-year = {2003}
-}
-@article{Broms2014,
-abstract = {Hill numbers unify biodiversity metrics by combining several into one expression. For example, species richness, Shannon's diversity index and the Gini–Simpson index are a few of the most used diversity measures, and they can be expressed as Hill numbers. Traditionally, Hill numbers have been calculated from relative abundance data, but the expression has been modified to use incidence data as well. We demonstrate an approach for estimating Hill numbers using an occupancy modelling framework that accounts for imperfect detection. We alter the Hill numbers formula to use occupancy probabilities as opposed to the incidence probabilities that have been used previously and to calculate its summations from the modelled species richness. After introducing the occupancy-based Hill numbers, we demonstrate the differences between them and the incidence-based Hill numbers previously used through a simulation study and two applications. In the simulation study and the two examples using real data, the occupancy-based Hill numbers were larger than the incidence-based Hill numbers, although species richness was estimated similarly using both methods. The occupancy-based Hill number estimators are always at their asymptotic values (i.e. as if an infinite number of samples have been taken for the study region), therefore making it easy to compare biodiversity between different assemblages. In addition, the Hill numbers are computed as derived quantities within a Bayesian hierarchical model, allowing for straightforward inference.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Broms, Kristin M. and Hooten, Mevin B. and Fitzpatrick, Ryan M.},
-doi = {10.1111/2041-210X.12296},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Broms, Hooten, Fitzpatrick - 2014 - Accounting for Imperfect Detection in Hill Numbers for Biodiversity Studies.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Broms, Hooten, Fitzpatrick - 2014 - Accounting for Imperfect Detection in Hill Numbers for Biodiversity Studies(2).pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {1},
-pages = {99--108},
-title = {{Accounting for Imperfect Detection in Hill Numbers for Biodiversity Studies}},
-url = {http://doi.wiley.com/10.1111/2041-210X.12296},
-volume = {6},
-year = {2014}
-}
-@article{Leinster2013,
-abstract = {Magnitude is a real-valued invariant of metric spaces, analogous to Euler characteristic of topological spaces and cardinality of sets. The definition of magnitude is a special case of a general categorical definition that clarifies the analogies between cardinality- like invariants in mathematics. Although this motivation is a world away from geometric measure, magnitude, when applied to subsets of Rn, turns out to be intimately related to invariants such as volume, surface area, perimeter and dimension. We describe several aspects of this relationship, providing evidence for a conjecture (first stated in joint work with Willerton) that magnitude encodes all the most important invariants of classical integral geometry.},
-author = {Leinster, Tom},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leinster - 2013 - The Magnitude of Metric Spaces.pdf:pdf},
-journal = {Documenta Mathematica},
-pages = {857--905},
-title = {{The Magnitude of Metric Spaces}},
-volume = {18},
-year = {2013}
-}
-@article{Petchey2006,
-abstract = {Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.},
-annote = {ISI Document Delivery No.: 043YD},
-author = {Petchey, Owen L. and Gaston, Kevin J.},
-doi = {10.1111/j.1461-0248.2006.00924.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Petchey, Gaston - 2006 - Functional diversity back to basics and looking forward.pdf:pdf},
-journal = {Ecology Letters},
-number = {6},
-pages = {741--758},
-title = {{Functional diversity: back to basics and looking forward}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2006.00924.x/abstract},
-volume = {9},
-year = {2006}
-}
-@book{Levins1968,
-abstract = {Professor Levins, one of the leading explorers in the field of integrated population biology, considers the mutual interpenetration and joint evolution of organism and environment, occurring on several levels at once. Physiological and behavioral adaptations to short-term fluctuations of the environment condition the responses of populations to long-term changes and geographic gradients. These in turn affect the way species divide the environments among themselves in communities, and, therefore, the numbers of species which can coexist. Environment is treated here abstractly as pattern: patchiness, variability, range, etc. Populations are studied in their patterns: local heterogeneity, geographic variability, faunistic diversity, etc.},
-author = {Levins, Richard},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Levins - 1968 - Evolution in Changing Environments Some Theoretical Explorations.pdf:pdf},
-isbn = {0-691-07959-5},
-publisher = {Princeton University Press},
-title = {{Evolution in Changing Environments: Some Theoretical Explorations}},
-year = {1968}
-}
-@article{Rodrigues2009,
-abstract = {The Brazilian Amazon is globally important for biodiversity, climate, and geochemical cycles, but is also among the least developed regions in Brazil. Economic development is often pursued through forest conversion for cattle ranching and agriculture, mediated by logging. However, on the basis of an assessment of 286 municipalities in different stages of deforestation, we found a boom-and-bust pattern in levels of human development across the deforestation frontier. Relative standards of living, literacy, and life expectancy increase as deforestation begins but then decline as the frontier evolves, so that pre- and postfrontier levels of human development are similarly low. New financial incentives and policies are creating opportunities for a more sustained development trajectory that is not based on the depletion of nature and ecosystem services.},
-author = {Rodrigues, Ana S. L. and Ewers, Robert M. and Parry, Luke and Souza, Carlos and Ver{\'{i}}ssimo, Adalberto and Balmford, Andrew},
-doi = {10.1126/science.1174002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rodrigues et al. - 2009 - Boom-and-Bust Development Patterns Across the Amazon Deforestation Frontier.pdf:pdf},
-journal = {Science},
-number = {5933},
-pages = {1435--1437},
-title = {{Boom-and-Bust Development Patterns Across the Amazon Deforestation Frontier}},
-url = {http://www.sciencemag.org/content/324/5933/1435.abstract},
-volume = {324},
-year = {2009}
-}
-@article{Espa2013,
-abstract = {A series of recent papers have introduced some explorative methods based on Ripley's K-function (Ripley in J R Stat Soc B 39(2):172-212, 1977) analyzing the micro-geographical patterns of firms. Often the spatial heterogeneity of an area is handled by referring to a case-control design, in which spatial clusters occur as over-concentrations of firms belonging to a specific industry as opposed to the distribution of firms in the whole economy. Therefore, positive, or negative, spatial dependence between firms occurs when a specific sector of industry is seen to present a more aggregated pattern (or more dispersed) than is common in the economy as a whole. This approach has led to the development of relative measures of spatial concentration which, as a consequence, are not straightforwardly comparable across different economies. In this article, we explore a parametric approach based on the inhomogeneous K-function (Baddeley et al. in Statistica Nederlandica 54(3):329-350, 2000) that makes it possible to obtain an absolute measure of the industrial agglomeration that is also able to capture spatial heterogeneity. We provide an empirical application of the approach taken with regard to the spatial distribution of high-tech industries in Milan (Italy) in 2001.},
-annote = {ISI Document Delivery No.: 063NP
-Times Cited: 0
-Cited Reference Count: 53
-Espa, Giuseppe Arbia, Giuseppe Giuliani, Diego
-Springer heidelberg
-Heidelberg},
-author = {Espa, Giuseppe and Arbia, Giuseppe and Giuliani, Diego},
-doi = {10.1007/s10109-012-0163-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Espa, Arbia, Giuliani - 2013 - Conditional versus unconditional industrial agglomeration disentangling spatial dependence and spatial he.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {1},
-pages = {31--50},
-title = {{Conditional versus unconditional industrial agglomeration: disentangling spatial dependence and spatial heterogeneity in the analysis of ICT firms' distribution in Milan}},
-volume = {15},
-year = {2013}
-}
-@book{Sen1997,
-address = {New York},
-annote = {Seconde version (augment{\'{e}}e) de son livre de 1973 "On Economic Inequality", Clarendon Press},
-author = {Sen, Amartya},
-edition = {Second Edi},
-publisher = {Clarendon Press, Oxford University Press},
-title = {{On Economic Inequality}},
-year = {1997}
-}
-@book{Greig-Smith1983,
-address = {Berkeley and Los Angeles},
-author = {Greig-Smith, Peter},
-edition = {3rd editio},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Greig-Smith - 1983 - Quantitative Plant Ecology.pdf:pdf},
-publisher = {University of California Press},
-title = {{Quantitative Plant Ecology}},
-year = {1983}
-}
-@article{Meziane2001,
-abstract = {We present a series of competing path models relating interspecific patterns between specific leaf area, leaf nitrogen content, net photosynthesis and stomatal conductance and test these against data from 22 species of herbaceous plants grown under controlled conditions with contrasting irradiance and nutrient supply rates. We then compare these results with two previous data sets, one based on field measures and one based on glasshouse measures, to determine the robustness of the results. Only one model was able to account for the patterns of direct and indirect effects between the four variables to all data sets. In this model specific leaf area is the forcing variable that directly affects both leaf nitrogen levels and net photosynthetic rates. Leaf nitrogen then directly affects net photosynthetic rates which in turn then affect stomatal conductance to water. (C) 2001 Annals of Botany Company.},
-author = {Meziane, Driss and Shipley, Bill},
-doi = {10.1006/anbo.2001.1536},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Meziane, Shipley - 2001 - Direct and indirect relationships between specific leaf area, leaf nitrogen and leaf gas exchange. Effects of.pdf:pdf},
-journal = {Annals of Botany},
-number = {5},
-pages = {915--927},
-title = {{Direct and indirect relationships between specific leaf area, leaf nitrogen and leaf gas exchange. Effects of irradiance and nutrient supply}},
-url = {https://doi.org/10.1006/anbo.2001.1536},
-volume = {88},
-year = {2001}
-}
-@article{Sokal1962,
-author = {Sokal, Robert R. and Rohlf, F. James},
-doi = {10.2307/1217208},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sokal, Rohlf - 1962 - The Comparison of Dendrograms by Objective Methods.pdf:pdf},
-journal = {Taxon},
-number = {2},
-pages = {33--40},
-title = {{The Comparison of Dendrograms by Objective Methods}},
-url = {http://www.jstor.org/stable/1217208},
-volume = {11},
-year = {1962}
-}
-@article{Visser2015,
-abstract = {Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.},
-author = {Visser, Marco D. and McMahon, Sean M. and Merow, Cory and Dixon, Philip M. and Record, Sydne and Jongejans, Eelke},
-doi = {10.1371/journal.pcbi.1004140},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Visser et al. - 2015 - Speeding Up Ecological and Evolutionary Computations in R Essentials of High Performance Computing for Biologists.PDF:PDF},
-journal = {PLoS Computational Biology},
-number = {3},
-pages = {e1004140},
-title = {{Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists}},
-url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004140},
-volume = {11},
-year = {2015}
-}
-@article{Garnier2004,
-abstract = {Although the structure and composition of plant communities is known to influence the functioning of ecosystems, there is as yet no agreement as to how these should be described from a functional perspective. We tested the biomass ratio hypothesis, which postulates that ecosystem properties should depend on species traits and on species contribution to the total biomass of the community, in a successional sere following vineyard abandonment in the Mediterranean region of France. Ecosystem-specific net primary productivity, litter decomposition rate, and total soil carbon and nitrogen varied significantly with field age, and correlated with community-aggregated (i.e., weighed according to the relative abundance of species) functional leaf traits. The three easily measurable traits tested, specific leaf area, leaf dry matter content, and nitrogen concentration, provide a simple means to scale up from organ to ecosystem functioning in complex plant communities. We propose that they be called “functional markers,” and be used to assess the impacts of community changes on ecosystem properties induced, in particular, by global change drivers.},
-author = {Garnier, Eric and Cortez, Jacques and Bill{\`{e}}s, Georges and Navas, Marie-Laure and Roumet, Catherine and Debussche, Max and Laurent, G{\'{e}}rard and Blanchard, Alain and Aubry, David and Bellmann, Astrid and Neill, Cathy and Toussaint, Jean-Patrick},
-doi = {10.1890/03-0799},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Garnier et al. - 2004 - Plant functional markers capture ecosystem properties during secondary succession.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2630--2637},
-title = {{Plant functional markers capture ecosystem properties during secondary succession}},
-url = {http://www.esajournals.org/doi/abs/10.1890/03-0799},
-volume = {85},
-year = {2004}
-}
-@misc{JournalofficieldelaRepubliquefrancaise1991,
-author = {{Journal officiel de la R{\'{e}}publique fran{\c{c}}aise}},
-title = {{Circulaire du 14 octobre 1991 relative {\`{a}} la gestion des parcs automobiles des administrations civiles et des {\'{e}}tablissements publics de l'{\'{E}}tat}},
-url = {http://www.dsi.cnrs.fr/RMLR/textesintegraux/volume5/553-cirdu14-10-1991.htm},
-year = {1991}
-}
-@article{Arbia2016a,
-abstract = {The presence of knowledge spillovers and shared human capital is at the heart of the Marhall–Arrow–Romer externalities hypothesis. Most of the earlier empirical contributions on knowledge externalities; however, considered data aggregated at a regional level so that conclusions are basedonthe arbitrary definition of jurisdictional spatial units: this is the essence of the so-called modifiable areal unit problem. A second limitation of these studies is constituted by the fact that, somewhat surprisingly, while concentrating on the effects of agglomeration on firm creation and growth, the literature has, conversely, largely ignored its effects on firm survival. The present paper aims at contributing to the existing literature by answering to some of the open methodological questions reconciling the literature of Cox proportional hazards model with that on point pat- tern and thus capturing the true nature of spatial information. We also present some empirical results based on Italian firm demogra- phy data collected and managed by the Italian National Institute of Statistics (ISTAT).},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Giuliani, Diego and Micciolo, Rocco},
-doi = {10.1080/02664763.2016.1214249},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2016 - A spatial analysis of health and pharmaceutical firm survival.pdf:pdf},
-journal = {Journal of Applied Statistics},
-number = {9},
-pages = {1560--1575},
-title = {{A spatial analysis of health and pharmaceutical firm survival}},
-url = {https://www.tandfonline.com/doi/full/10.1080/02664763.2016.1214249},
-volume = {44},
-year = {2017}
-}
-@article{Wilson1984,
-abstract = {(1) Six measures of beta diversity (five from the literature, one proposed here) were compared and evaluated. Application was limited to measures suited for species presence-absence data along environmental gradients. (2) Four ecological criteria of 'good' performance of beta diversity measures were developed: (i) conformity with the notion of community turnover ensures that the magnitude of a measure is meaningful; (ii) additivity is the property that the sum of beta diversities between contiguous segments equals the beta diversity of the entire gradient; (iii) independence from alpha diversity ensures useful application of a measure to systems with different alpha diversities; (iv) independence from excessive sample size obviates any spurious effects of oversampling. (3) Two measures of beta diversity (one proposed by Whittaker (1960) and one proposed in the present paper) came closest to fulfilling all four criteria and should be of most use in ecological applications. (4) Field data from Mt Hermon in Israel were used to compare the usefulness of the six measures. (5) Current problems and issues, including the relationship between species-area curves and beta diversity, and future applications in measuring beta diversity are discussed.},
-author = {Wilson, M. V. and Shmida, A.},
-doi = {10.2307/2259551},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilson, Shmida - 1984 - Measuring Beta Diversity with Presence-Absence Data.pdf:pdf},
-journal = {The Journal of Ecology},
-number = {3},
-pages = {1055},
-title = {{Measuring Beta Diversity with Presence-Absence Data}},
-url = {http://www.jstor.org/stable/2259551?origin=crossref},
-volume = {72},
-year = {1984}
-}
-@article{Chao1984,
-abstract = {Assume that a random sample is drawn frent a population with an unknown number of classes. This work proposes a nonparametric method to estimate the number of classes when most of the information is concentrated on the low order occupancy numbers. The percentile method (Efron, 1981, 1982) is applied to construct confidence intervals based on bootstrap distributions. Using real data sets, we also compare the proposed point and interval estimates with previously published results.},
-author = {Chao, Anne},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao - 1984 - Nonparametric estimation of the number of classes in a population.pdf:pdf},
-journal = {Scandinavian Journal of Statistics},
-number = {4},
-pages = {265--270},
-title = {{Nonparametric estimation of the number of classes in a population}},
-url = {http://www.jstor.org/stable/4615964},
-volume = {11},
-year = {1984}
-}
-@article{Laliberte2010,
-abstract = {A new framework for measuring functional diversity (FD) from multiple traits has recently been proposed. This framework was mostly limited to quantitative traits without missing values and to situations in which there are more species than traits, although the authors had suggested a way to extend their framework to other trait types. The main purpose of this note is to further develop this suggestion. We describe a highly flexible distance-based framework to measure different facets of FD in multidimensional trait space from any distance or dissimilarity measure, any number of traits, and from different trait types (i.e., quantitative, semi-quantitative, and qualitative). This new approach allows for missing trait values and the weighting of individual traits. We also present a new multidimensional FD index, called functional dispersion (FDis), which is closely related to Rao's quadratic entropy. FDis is the multivariate analogue of the weighted mean absolute deviation (MAD), in which the weights are species relative abundances. For unweighted presence–absence data, FDis can be used for a formal statistical test of differences in FD. We provide the ‘‘FD'' R language package to easily implement our distance-based FD framework.},
-author = {Lalibert{\'{e}}, Etienne and Legendre, Pierre},
-doi = {10.1890/08-2244.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lalibert{\'{e}}, Legendre - 2010 - A distance-based framework for measuring functional diversity from multiple traits.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {299--305},
-title = {{A distance-based framework for measuring functional diversity from multiple traits}},
-volume = {91},
-year = {2010}
-}
-@incollection{Prance1983,
-author = {Prance, G T},
-booktitle = {Ecosystem of the world},
-pages = {99--132},
-title = {{American tropical forest}},
-year = {1983}
-}
-@article{Batista1998,
-abstract = {The spatial structure of tropical forest stands under different management conditions was modeled as a series of different spatial point processes. Spatial patterns were first assessed by K-function analyses to help choose a point process appropriate for observed patterns. The homogenous Neyman-Scott process accurately described live tree distribution in clear cut areas, where tree patterns tended to be aggregated. Parameters were estimated by minimizing Diggle's modified least squares criterion, and goodness-of-fit was assessed by comparison to confidence envelopes constructed by Monte Carlo simulation. Parameter estimates can be interpreted to help understand the ecological processes influencing re-colonization of disturbed areas. The inhomogeneous Poisson process was investigated for simulating the spatial pattern of ingrowth trees in lower canopy strata. The intensity function of this process was inversely proportional to variables representing canopy density. As assessed by Monte Carlo generation of confidence envelopes, the inhomogeneous Poisson process successfully portrayed the influence of canopy structure on understory plant distribution in most stands. Tree mortality was modeled as a thinning process in which the probability of individual tree mortality was conditional on subject tree attributes and competitive environment. The thinning function took the form of a generalized linear model with a binomial error distribution and logit link function. In most stands, tree neighborhood variables were powerful predictors of mortality, but they were not important predictors in all plots. This suggests that the surrounding forest structure of a subject tree has considerable influence on its morality, but competition is not the sole cause of tree morality in tropical forests.},
-author = {Batista, Jo{\~{a}}o Luiz Ferreira and Maguire, Douglas A},
-doi = {10.1016/S0378-1127(98)00296-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Batista, Maguire - 1998 - Modelling the spatial structure of tropical forests.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {293--314},
-title = {{Modelling the spatial structure of tropical forests}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112798002965},
-volume = {110},
-year = {1998}
-}
-@article{Tuomisto2006,
-abstract = {It has been actively discussed recently what statistical methods are appropriate when one is interested in testing hypotheses about the origin of beta diversity, especially whether one should use the raw-data approach (e.g., canonical analysis such as RDA and CCA) or the distance approach (e.g., Mantel test and multiple regression on distance matrices). Most of the confusion seems to stem from uncertainty as to what is the response variable in the different approaches. Here our aim is to clarify this issue. We also show that, although both the raw-data approach and the distance approach can often be used to address the same ecological hypothesis, they target fundamentally different predictions of those hypotheses. As the two approaches shed light on different aspects of the ecological hypotheses, they should be viewed as complementary rather than alternative ways of analyzing data. However, in some cases only one of the approaches may be appropriate. We argue that S. P. Hubbell's neutral theory can only be tested using the distance approach, because its testable predictions are stated in terms of distances, not in terms of raw data. In all cases, the decision on which method is chosen must be based on which addresses the question at hand, it cannot be based on which provides the highest proportion of explained variance in simulation studies.},
-author = {Tuomisto, Hanna and Ruokolainen, Kalle},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto, Ruokolainen - 2006 - Analyzing or explaining beta diversity Understanding the targets of different methods of analysis.pdf:pdf},
-journal = {Ecology},
-number = {11},
-pages = {2697--2708},
-title = {{Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis}},
-url = {http://www.esajournals.org/doi/abs/10.1890/0012-9658(2006)87{\%}255B2697:AOEBDU{\%}255D2.0.CO{\%}253B2},
-volume = {87},
-year = {2006}
-}
-@incollection{Terborgh1992,
-abstract = {Evolutionary dynamics The allopatric model of speciation The great American faunal interchange Milankovitch cycles and a possible speciation pump Tropical diversity: the general case},
-author = {Terborgh, John},
-booktitle = {Diversity and the Tropical Rain Forest},
-pages = {131--152},
-title = {{The evolution of diversity}},
-year = {1992}
-}
-@article{Diggle1995,
-abstract = {We consider the problem of detecting and describing space-time interaction in point process data. We extend existing second-order methods for purely spatial point process data to the spatial-temporal setting. This extension allows us to estimate space-time interaction as a function of spatial and temporal separation, and provides a useful reinterpretation of a popular test, due to Knox, for space-time interaction. Applications to simulated and real data indicate the method's potential.},
-author = {Diggle, Peter J. and Chetwynd, A. G. and H{\"{a}}ggkvist, R. and Morris, Sara E.},
-doi = {10.1177/096228029500400203},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle et al. - 1995 - Second-order analysis of space-time clustering.pdf:pdf},
-journal = {Statistical Methods in Medical Research},
-number = {2},
-pages = {124--126},
-title = {{Second-order analysis of space-time clustering}},
-url = {http://journals.sagepub.com/doi/abs/10.1177/096228029500400203},
-volume = {4},
-year = {1995}
-}
-@article{Hedrick2005,
-abstract = {Interpretation of genetic differentiation values is often problematic because of their dependence on the level of genetic variation. For example, the maximum level of GST is less than the average within population ho- mozygosity so that for highly variable loci, even when no alleles are shared between subpopulations, GST may be low. To remedy this difficulty, a standardized measure of genetic differentiation is introduced here, one which has the same range, 0–1, for all levels of genetic variation. With this measure, the magnitude is the proportion of the maximum differentiation possible for the level of subpopulation homozygosity observed. This is particularly important for situations in which the mutation rate is of the same magnitude or higher than the rate of gene flow. The standardized measure allows comparison between loci with different levels of genetic variation, such as allozymes and microsatellite loci, or mtDNA and Y-chromosome genes, and for genetic differentiation for organisms with different effective population sizes.},
-author = {Hedrick, Philip W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hedrick - 2005 - A standardized genetic differentiation measure.pdf:pdf},
-journal = {Evolution},
-number = {8},
-pages = {1633--1638},
-title = {{A standardized genetic differentiation measure}},
-volume = {59},
-year = {2005}
-}
-@article{Mori2015,
-abstract = {Standard approaches to studying industrial agglomeration have been in terms of scalar measures of agglomeration within each industry. But such measures often fail to distinguish spatial scales of agglom- eration. In a previous paper, Mori and Smith (2014) proposed a pair of quantitative measures for distin- guishing both the scale and degree of industrial agglomeration based on an explicit method for detecting spatial clusters. The first, designated as the global extent of industrial clusters, measures the spatial spread of these clusters in terms of the areal size of their essential containment, defined to be the (convex-solid) region containing the most significant subset of these clusters. The second, designated as the local density of industrial clusters, measures the spatial extent of individual clusters within their essential containment in terms of the areal share of that containment occupied by clusters. The present paper applies this pair of measures to manufacturing industries in Japan, and the results obtained are systematically compared to those of the most prominent scalar measures currently in use. Finally, these measures are shown to sup- port certain predictions of new economic geography models concerning the relationship between ship- ment distances and spatial scales of agglomeration for individual industries.},
-author = {Mori, Tomoya and Smith, Tony E.},
-doi = {10.1016/j.jue.2015.01.006},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mori, Smith - 2015 - On the spatial scale of industrial agglomerations.pdf:pdf},
-journal = {Journal of Urban Economics},
-pages = {1--20},
-title = {{On the spatial scale of industrial agglomerations}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0094119015000078},
-volume = {89},
-year = {2015}
-}
-@article{Dallot2003,
-abstract = {The spatial pattern of Sharka disease, caused by Plum pox virus (PPV) strain M, was investigated in 18 peach plots located in two areas of southern France. PPV infections were monitored visually for each individual tree during one to three consecutive years. Point pattern and correlation-type approaches were undertaken using the binary data directly or after parsing them in contiguous quadrats of 4, 9, and 16 trees. Ordinary runs generally revealed a low but variable proportion of rows with adjacent symptomatic trees. Aggregation of disease incidence was indicated by the theta parameter of the beta-binomial distribution and related indices in 15 of the 18 plots tested for at least one assessment date of each. When aggregation was detected, it was indicated at all quadrat sizes and tended to be a function of disease incidence, as shown by the binary form of Taylor's power law. Spatial analysis by distance indices (SADIE) showed a nonrandom arrangement of quadrats with infected trees in 14 plots. The detection of patch clusters enclosing quadrats with above-average density of symptomatic trees, ellipsoidal in shape and generally extending from 4 to 14 trees within rows and from 4 to 10 trees perpendicular to the rows, could be interpreted as local areas of influence of PPV spread. Spatial patterns at the plot scale were often characterized by the occurrence of several clusters of infected trees located up to 90 m apart in the direction of the rows. When several time assessments were available, increasing clustering over time was generally evidenced by stronger values of the clustering index and by increasing patch cluster size. The combination of the different approaches revealed a wide range of spatial patterns of PPV-M, from no aggregation to high aggregation of symptomatic trees at all spatial scales investigated. Such patterns suggested that aphid transmission to neighboring trees occurred frequently but was not systematic. The mechanism of primary virus introduction, the age and structure of the orchards when infected, and the diversity of vector species probably had a strong influence on the secondary spread of the disease. This study provides a more complete understanding of PPV-M patterns which could help to improve targeting of removal of PPV-infected trees for more effective disease control.},
-annote = {Article},
-author = {Dallot, S. and Gottwald, Tim R. and Labonne, G. and Quiot, J. B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dallot et al. - 2003 - Spatial pattern analysis of sharka disease (Plum pox virus strain M) in peach orchards of southern France.pdf:pdf},
-journal = {Phytopathology},
-number = {12},
-pages = {1543--1552},
-title = {{Spatial pattern analysis of sharka disease (Plum pox virus strain M) in peach orchards of southern France}},
-volume = {93},
-year = {2003}
-}
-@article{Shannon1948,
-author = {Shannon, Claude E},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shannon - 1948 - A Mathematical Theory of Communication.pdf:pdf},
-journal = {The Bell System Technical Journal},
-pages = {379--423, 623--656},
-title = {{A Mathematical Theory of Communication}},
-volume = {27},
-year = {1948}
-}
-@incollection{McFadden1984,
-address = {Amsterdam},
-author = {McFadden, Daniel},
-booktitle = {Handbook of Econometrics},
-editor = {Griliches, Z and Intriligator, M D},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McFadden - 1984 - Econometric Analysis of Qualitative Response Models.pdf:pdf},
-publisher = {Elsevier},
-title = {{Econometric Analysis of Qualitative Response Models}},
-volume = {II},
-year = {1984}
-}
-@article{Felsenstein1985,
-abstract = {Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.},
-author = {Felsenstein, Joseph},
-doi = {10.1086/284325},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Felsenstein - 1985 - Phylogenies and the Comparative Method.pdf:pdf},
-journal = {The American Naturalist},
-number = {1},
-pages = {1--15},
-title = {{Phylogenies and the Comparative Method}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/284325},
-volume = {25},
-year = {1985}
-}
-@article{Gerard1996,
-abstract = {La base de donn{\'{e}}es technologie reprend tous les essais effectu{\'{e}}s par les laboratoires du CIRAD-For{\^{e}}t.},
-author = {G{\'{e}}rard, J. and Narboni, Ph.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/G{\'{e}}rard, Narboni - 1996 - Une base de donn{\'{e}}es sur les propri{\'{e}}t{\'{e}}s technologiques des bois.pdf:pdf},
-journal = {Bois et for{\^{e}}t des tropiques},
-pages = {65--70},
-title = {{Une base de donn{\'{e}}es sur les propri{\'{e}}t{\'{e}}s technologiques des bois}},
-url = {http://agritrop.cirad.fr/388248/},
-volume = {248},
-year = {1996}
-}
-@article{Poorter1999,
-abstract = {1. Growth of seedlings of 15 rain-forest tree species was compared under controlled conditions, at six different light levels (3, 6, 12, 25, 50 and 100{\%} daylight). 2. Most plant variables showed strong ontogenetic changes; they were highly dependent on the biomass of the plant. 3. Growth rate was highest at intermediate fight levels (25-50{\%}) above which it declined. Most plant variables showed a curvilinear response to irradiance, with the largest changes at the lowest Light levels. 4. There was a consistent ranking in growth between species; species that were fast growing in a low-light environment were also fast growing in a high-light environment. 5. At low light, interspecific variation in relative growth rate was determined mainly by differences in a morphological trait, the leaf area ratio (LAR), whereas at high light it was determined mainly by differences in a physiological trait, the net assimilation rate (NAR). 6. NAR became a stronger determinant of growth than LAR in more than 10-15{\%} daylight. As light availability in the forest is generally much lower than this threshold level, it follows that interspecific variation in growth in a forest environment is mainly owing to variation in morphology.},
-annote = {JUN
-FUNCT ECOL},
-author = {Poorter, Lourens},
-doi = {10.1046/j.1365-2435.1999.00332.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Poorter - 1999 - Growth responses of 15 rain-forest tree species to a light gradient the relative importance of morphological and physio.pdf:pdf},
-journal = {Functional Ecology},
-number = {3},
-pages = {396--410},
-title = {{Growth responses of 15 rain-forest tree species to a light gradient: the relative importance of morphological and physiological traits}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2435.1999.00332.x/abstract},
-volume = {13},
-year = {1999}
-}
-@article{Duranton2015,
-abstract = {This review discusses frontier topics in economic geography as they relate to firms and agglomeration economies. We focus on areas where empirical research is scarce but possible. We first outline a conceptual framework for city formation that allows us to contemplate what empiricists might study when using firm-level data to compare the functioning of cities and industries with each other. We then examine a second model of the internal structure of a cluster to examine possibilities with firm-level data for better exposing the internal operations of clusters. An overwhelming theme of our review is the vast scope for enhancements of our picture of agglomeration with the new data that are emerging.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Duranton, Gilles and Kerr, William R},
-doi = {10.3386/w21452},
-eprint = {arXiv:1011.1669v3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Duranton, Kerr - 2015 - The Logic of Agglomeration.pdf:pdf},
-journal = {NBER Working Paper},
-title = {{The Logic of Agglomeration}},
-volume = {21452},
-year = {2015}
-}
-@article{Gotelli2001,
-abstract = {Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category–subcategory ratios (species-to-genus and species-to-individual ratios). Rarefaction methods – both sample-based and individual-based – allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower-bound estimates for taxon-rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Gotelli, Nicholas J. and Colwell, Robert K.},
-doi = {10.1046/j.1461-0248.2001.00230.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gotelli, Colwell - 2001 - Quantifying biodiversity procedures and pitfalls in the measurement and comparison of species richness.pdf:pdf},
-journal = {Ecology Letters},
-number = {4},
-pages = {379--391},
-title = {{Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness}},
-url = {http://dx.doi.org/10.1046/j.1461-0248.2001.00230.x},
-volume = {4},
-year = {2001}
-}
-@article{Saunders1977,
-abstract = {In this article we present a limiting result for the random variable Yn(r) which arises in a clustering model of Strauss (1975). The result is that under some sparseness-of-points conditions the process {\{}Yn(r):0≤ r≤ r00{\}} converges weakly to a non-homogeneous Poisson process {\{}Y(r):0≤ r≤ r00{\}} when n → ∞. Simulation results are given to indicate the accuracy of the approximation when n is moderate and applications of the limiting result to tests for clustering are discussed.},
-author = {Saunders, Roy},
-doi = {10.1017/S0021900200105303},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Saunders - 1977 - Poisson Limits for a Clustering Model of Strauss.pdf:pdf},
-journal = {Journal of Applied Probability},
-pages = {776--784},
-title = {{Poisson Limits for a Clustering Model of Strauss}},
-url = {https://doi.org/10.1017/S0021900200105303},
-volume = {14},
-year = {1977}
-}
-@article{Burnham1979,
-abstract = {A model is given for multiple recapture studies on closed populations which allows capture probabilities to vary among individuals. The capture probability of each individual is assumed to be constant over time. Based on this model we give a nonparametric estimation procedure for population size. The estimator involves selecting one of a sequence of estimators which are each linear combinations of the capture frequencies. The individual estimators are derived from the generalized jackknife method. We also give a goodness of fit test for the model's assumption that individual capture probabilities do not change during the study. The robustness of this estimation procedure is investigated with a simulation study. By virtue of this study, and the theoretical nature of the estimator, it is judged to be robust to moderate variations in individual capture probabilities which may occur in commonly used short—term livetrapping studies.},
-author = {Burnham, K. P. and Overton, W. S.},
-doi = {10.2307/1936861},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Burnham, Overton - 1979 - Robust Estimation of Population Size When Capture Probabilities Vary Among Animals.pdf:pdf},
-journal = {Ecology},
-number = {5},
-pages = {927--936},
-title = {{Robust Estimation of Population Size When Capture Probabilities Vary Among Animals}},
-url = {http://www.jstor.org/stable/1936861},
-volume = {60},
-year = {1979}
-}
-@misc{UniversitedesAntillesetdelaGuyane-CRIGuyane2009,
-author = {{Universit{\'{e}} des Antilles et de la Guyane - CRI Guyane}},
-title = {{Charte pour l'utilisation des ressources r{\'{e}}seau et internet g{\'{e}}r{\'{e}}es par le CRI-UG}},
-url = {https://intranet.ecofog.gf/IMG/pdf/CharteInfoUAG112{\_}v2.pdf},
-year = {2009}
-}
-@article{Steinitz2005,
-abstract = {In a review of recent challenges in conservation planning, Ferrier (2002) proposed the incorporation of models of similarity in species composition as a means for prioritizing areas for biodiversity conservation. A key assumption of this approach is that estimates of compositional similarity derived from models of similarity in species composition can be used as effective surrogates for real similarity data. We used data on snail distribution in Israel to test this assumption. We used two types of models to analyze patterns of similarity in species composition. one based on presence/absence data and the second based on abundance data. Both models accounted for large amounts of The observed variation in compositional similarity. Variation-partitioning analysis indicated that a considerable amount of the variation in compositional similarity could be separated into "pure" geographical versus "pure" environmental components, indicating that reserve selection procedures should take into account spatial considerations in determining priorities for conservation. The relative effects of geographical versus environmental factors varied between the two types of models, indicating that different indices of similarity should. be used if one wishes to represent species composition per se or ecological communities including their relative species abundances. A comparison of distribution patterns of land snails and land birds in a subset of the study sites revealed a high degree of congruence in compositional similarity between the two groups. Moreover, compositional similarity in snails was a better predictor of compositional similarity in birds compared with all environmental and geographical distances taken together Models calibrated based on delta collected in small plots explained a considerable amount of the variation observed at larger scales, suggesting that sampling efforts required for conservation planning might be lower (and thus, more feasible) than assumed previously Models of similarity in species composition may serve as all important tool for conservation planning.},
-annote = {ISI Document Delivery No.: 993ET
-Times Cited: 22
-Cited Reference Count: 70
-BLACKWELL PUBLISHING},
-author = {Steinitz, Ofer and Heller, Joseph and Tsoar, Asaf and Rotem, Dotan and Kadmon, Ronen},
-doi = {10.1111/j.1523-1739.2005.00237.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Steinitz et al. - 2005 - Predicting regional patterns of similarity in species composition for conservation planning.pdf:pdf},
-journal = {Conservation Biology},
-number = {6},
-pages = {1978--1988},
-title = {{Predicting regional patterns of similarity in species composition for conservation planning}},
-volume = {19},
-year = {2005}
-}
-@article{Tuomisto2010b,
-abstract = {The present two-part review aims to put the different phenomena that have been called "beta diversity" over the years into a common conceptual framework and to explain what each of them measures. The first part (Tuomisto 2010) discussed basic definitions of "beta diversity". Each arises from a different way of combining a definition of "diversity" with a definition of its alpha component and with a mathematical relationship between the alpha and gamma components. This second part assumes that an appropriate basic definition of a beta component (which may or may not be true beta diversity) has been chosen, and the focus here will be on how to quantify it for a given dataset. About twenty different approaches have been used for this purpose. It turns out that only two of these approaches accurately quantify the selected beta component: one does so for the entire dataset, and the other for two sampling units at a time. The other approaches actually quantify other phenomena, such as mean species turnover between sampling units, compositional gradient length (with or without reference to an external gradient), distinctness of a focal sampling unit, rate of species accumulation with increasing sampling effort, rate of compositional turnover along an external gradient, or the rate of decay in compositional similarity with increasing geographical distance. Although most of these phenomena can be expressed as a function of a beta component of diversity, they do not equal a beta component of diversity. Many of these derived variables are not even numerically correlated with the beta component on which they are based, which needs to be taken into account when interpreting the results. The effects of sampling decisions when results are extrapolated beyond the available data will also be discussed.},
-annote = {Tuomisto, Hanna},
-author = {Tuomisto, Hanna},
-doi = {10.1111/j.1600-0587.2009.06148.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto - 2010 - A diversity of beta diversities straightening up a concept gone awry. Part 2. Quantifying beta diversity and related p.pdf:pdf},
-journal = {Ecography},
-number = {1},
-pages = {23--45},
-title = {{A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2009.06148.x/abstract},
-volume = {33},
-year = {2010}
-}
-@article{Ricotta2003,
-abstract = {Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a give community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.},
-annote = {Ricotta, C},
-author = {Ricotta, Carlo},
-doi = {10.1023/a:1025142106292},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta - 2003 - Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity A.pdf:pdf},
-journal = {Acta Biotheoretica},
-number = {3},
-pages = {181--188},
-title = {{Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: A first proposal using Shannon's entropy}},
-volume = {51},
-year = {2003}
-}
-@article{Podani1997,
-abstract = {On the basis of Ripley's combined count-distance method, Juhasz-Nagy's information theoretical functions and the proposition of Williams et al. for the study of small-scale community pattern, a new procedure is suggested for eluci- dating multi-species point patterns based on digitized field data. The method utilizes nested circular plots with increas- ing radii drawn around each individual and determines changes in floristic composition along this space series. The information provided by detecting the species composition around the sample plant is calculated, and its observed mean for all individuals is compared, for each radius, to the expec- tation under the null model, i.e. for complete spatial random- ness of all points. The departure from randomness is illus- trated by conventional profile diagrams and is tested for significance based on confidence envelopes simulated by Monte Carlo methods. One advantage of the individual- centered sampling strategy is that the role of each species in influencing its own neighbourhood can be analyzed sepa- rately, providing information for the assessment of guild structure and assembly rules in communities. The perform- ance of the method is evaluated using artificial and simulated point patterns},
-author = {Podani, J{\'{a}}nos and Cz{\'{a}}r{\'{a}}n, Tam{\'{a}}s},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {259--270},
-title = {{Individual-centered analysis of mapped point patterns representing multi-species assemblages}},
-volume = {8},
-year = {1997}
-}
-@article{Stier2016,
-abstract = {Beta diversity describes how species composition varies across space and through time. Current estimators of beta diversity typically ignore the effects of within-patch sample size, determined jointly by local abundance and sampling effort. Many ecological processes such as immigration, predation, or nutrient limitation affect abundance and asymptotic beta diversity concurrently; thus, existing metrics may confound changes in asymptotic beta diversity with changes that result from differences in abundance or sampling. Results from a stochastic simulation model illustrate how decreasing within-patch sample size may either increase or decrease observed beta diversity, depending on the type of metric, sample size, and community properties; these changes are easy to understand, and predict, by considering the effects of sampling on variance. A modi fi ed, patch-level form of rarefaction controls for variation in within-patch sample size; two case studies illustrate the utility of this approach. Studies seeking a mechanistic link between ecological process and beta diversity will continue to bene fi t from explicit consideration of sampling effects.},
-author = {Stier, Adrian C. and Bolker, Benjamin M. and Osenberg, Craig W.},
-doi = {10.1002/ecs2.1612},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stier, Bolker, Osenberg - 2016 - Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity.pdf:pdf},
-journal = {Ecosphere},
-number = {12},
-pages = {e01612},
-title = {{Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity}},
-url = {http://doi.wiley.com/10.1002/ecs2.1612},
-volume = {7},
-year = {2016}
-}
-@article{DeForesta1986,
-abstract = {The study of the relationship between pioneer vegetation and dormant seeds in the soil in the area of the St. Elie track, French Guiana, shows that: 1. In all points of the primary forest, one finds a major seed stock of pioneer species (150 to 200 seeds/M2); the proximity of pioneer vegetation creates a substantial increase of the seed stock in a comparatively narrow strip of soil (doubling of the seeds within 50 m, but the seed stock ratio is unchanged between 500 and 6000 m). 2. Adult pioneers in old forest gaps further stock heterogeneity through major enrichment in a limited area which may cover a 30-m range or more. 3. The stock evolves rapidly in the first years following the primary forest clearing, it is quantitatively replenished from the second year onwards, and after nine years, it is 4 to 5 times greater than in the primary forest, enriched with short-lived and early- bearing pioneer species, but impoverished in long-lived and late-bearing species. A},
-author = {de Foresta, Hubert and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/de Foresta, Pr{\'{e}}vost - 1986 - V{\'{e}}g{\'{e}}tation pionni{\`{e}}re et graines du sol en for{\^{e}}t guyanaise.pdf:pdf},
-journal = {Biotropica},
-number = {4},
-pages = {279--286},
-title = {{V{\'{e}}g{\'{e}}tation pionni{\`{e}}re et graines du sol en for{\^{e}}t guyanaise}},
-volume = {18},
-year = {1986}
-}
-@article{Botta-Dukat2017,
-abstract = {The replication principle was first proposed by Hill (1973) as an advantageous property of his family of diversity indices. Later Jost (2007) discovered that diversity measures satisfying this principle allow partitioning of gamma diversity into independent alpha and beta components by simple multiplicative partitioning. Despite the emerging agreement on measuring taxonomic beta-diversity by multiplicative partitioning of Hill diversity, there is no consensus on how to measure functional beta diversity. Two different generalizations of Hill numbers for measuring functional diversity were proposed by Leinster {\&} Cobbold (2011) and Chiu {\&} Chao (2014). Both generalizations attempted to satisfy the generalized replication principle, but they formulate it in different ways. The aims of this paper are (1) to review approaches for measuring functional diversity in units of equivalent numbers without explicit reference to replication principle; (2) to compare the two proposed replication principle and to point out some important differences in the behavior of diversity families derived from the two principles; (3) to explore the conditions necessary for partitioning functional diversity of Leinster {\&} Cobbold (2011) into meaningful alpha and beta components; (4) and, finally, to explore how transformation of among-species distances into similarities influences the sensitivity of functional diversity to the scale parameter.},
-author = {Botta-Duk{\'{a}}t, Zolt{\'{a}}n},
-doi = {10.1111/ecog.02009},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Botta-Duk{\'{a}}t - 2017 - The generalized replication principle and the partitioning of functional diversity into independent alpha and beta.pdf:pdf},
-journal = {Ecography},
-title = {{The generalized replication principle and the partitioning of functional diversity into independent alpha and beta components}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02009/full},
-volume = {in press},
-year = {2017}
-}
-@article{Mangan2010,
-abstract = {The accumulation of species-specific enemies around adults is hypothesized to maintain plant diversity by limiting the recruitment of conspecific seedlings relative to heterospecific seedlings. Although previous studies in forested ecosystems have documented patterns consistent with the process of negative feedback, these studies are unable to address which classes of enemies (for example, pathogens, invertebrates, mammals) exhibit species-specific effects strong enough to generate negative feedback, and whether negative feedback at the level of the individual tree is sufficient to influence community-wide forest composition. Here we use fully reciprocal shade-house and field experiments to test whether the performance of conspecific tree seedlings (relative to heterospecific seedlings) is reduced when grown in the presence of enemies associated with adult trees. Both experiments provide strong evidence for negative plant-soil feedback mediated by soil biota. In contrast, above-ground enemies (mammals, foliar herbivores and foliar pathogens) contributed little to negative feedback observed in the field. In both experiments, we found that tree species that showed stronger negative feedback were less common as adults in the forest community, indicating that susceptibility to soil biota may determine species relative abundance in these tropical forests. Finally, our simulation models confirm that the strength of local negative feedback that we measured is sufficient to produce the observed community-wide patterns in tree-species relative abundance. Our findings indicate that plant-soil feedback is an important mechanism that can maintain species diversity and explain patterns of tree-species relative abundance in tropical forests.},
-author = {Mangan, Scott A. and Schnitzer, Stefan A. and Herre, Edward A. and Mack, Keenan M. L. and Valencia, Mariana C. and Sanchez, Evelyn I. and Bever, James D.},
-doi = {10.1038/nature09273},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mangan et al. - 2010 - Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest.pdf:pdf},
-journal = {Nature},
-number = {7307},
-pages = {752--5},
-title = {{Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/20581819},
-volume = {466},
-year = {2010}
-}
-@article{Prance1990,
-author = {Prance, G T},
-journal = {Nature},
-number = {6274},
-pages = {384--384},
-title = {{Consensus for conservation}},
-volume = {345},
-year = {1990}
-}
-@article{Muller2014,
-abstract = {Ecologists have long recognized the important role of canopy heterogeneity in structuring the diversity of animal communities. However, studies directly linking variation in the three-dimensional structure of forests to variation in biodiversity are still rare. For canopy arthropods representing a dominant component of forest biodiversity in montane spruce forests of Europe, we used publicly available airborne LiDAR measurements to test the premises of two existing hypotheses that resource concentration and habitat heterogeneity are potential drivers of faunal diversity at both the tree scale and stand scale. We sampled 391 arthropod species from the canopies of 60 trees; coverage-based rarefaction revealed high completeness of faunal sampling (93.7{\%}). When we controlled for elevation and broadleaf tree cover, we found strong (tree and stand scale) context dependence in the response of arthropod diversity to variation in vegetation structure. Arthropod diversity increased with increasing canopy density at the tree scale and was positively associated only with vegetation heterogeneity at the tree scale, but decreased with increasing canopy density at the stand scale. These trends held across all levels of biological response from total richness to diversity measures to richness of different guilds. Our results showed that different components of vegetation structural complexity drive canopy arthropod biodiversity at different spatial scales. Highest canopy arthropod diversity can be expected in spruce forests with relatively open stands containing individual trees with dense and long crowns. Thus, LiDAR opens new avenues for testing ecological hypotheses and for forest-growth models to be linked with the canopy diversity of forests. (C) 2013 Elsevier B.V. All rights},
-annote = {ISI Document Delivery No.: 277EV
-Times Cited: 0
-Cited Reference Count: 70
-Mueller, Joerg Bae, Soyeon Roeder, Juliane Chao, Anne Didham, Raphael K.
-Australian Research Council Future Fellowship [FT100100040]; Taiwan National Science Council [100-2118-M007-006]
-We thank Marco Heurich and Karin Most for providing the airborne LiDAR data and associated information. We thank T.C. Hsieh for computational help. RKD was supported during the writing of this manuscript by an Australian Research Council Future Fellowship (FT100100040). AC is supported by Taiwan National Science Council under Contract 100-2118-M007-006.
-Elsevier science bv
-Amsterdam},
-author = {Muller, J. and Bae, S. and Roder, J. and Chao, Anne and Didham, Raphael K.},
-doi = {10.1016/j.foreco.2013.10.014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Muller et al. - 2014 - Airborne LiDAR reveals context dependence in the effects of canopy architecture on arthropod diversity.pdf:pdf},
-journal = {Forest Ecology and Management},
-pages = {129--137},
-title = {{Airborne LiDAR reveals context dependence in the effects of canopy architecture on arthropod diversity}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112713006816},
-volume = {312},
-year = {2014}
-}
-@article{Diggle2000,
-abstract = {The paper compares non-parametric (design-based) and parametric (model-based) approaches to the analysis of data in the form of replicated spatial point patterns in two or more experimental groups. Basic questions for data of this kind concern estimating the properties of the underlying spatial point process within each experimental group, and comparing the properties between groups. A non-parametric approach, building on work by Diggle et al. (1991), summarizes each pattern by an estimate of the reduced second moment measure or K-function (Ripley (1977)) and compares mean K-functions between experimental groups using a bootstrap testing procedure. A parametric approach fits particular classes of parametric model to the data, uses the model parameter estimates as summaries and tests for differences between groups by comparing fits with and without the assumption of common parameter values across groups. The paper discusses how either approach can be implemented in the specific context of a single-factor replicated experiment and uses simulations to show how the parametric approach can be more efficient when the underlying model assumptions hold, but potentially misleading otherwise.},
-annote = {Article
-English
-ADVAN APPL PROBAB
-342YB},
-author = {Diggle, Peter J. and Mateu, Jorge and Clough, Helene E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle, Mateu, Clough - 2000 - A comparison between parametric and non-parametric approaches to the analysis of replicated spatial point.pdf:pdf},
-journal = {Advances in Applied Probability},
-number = {2},
-pages = {331--343},
-title = {{A comparison between parametric and non-parametric approaches to the analysis of replicated spatial point patterns}},
-url = {http://www.jstor.org/stable/1428191},
-volume = {32},
-year = {2000}
-}
-@article{Billington1999,
-abstract = {In this piece of research, those factors are analysed which determine the choice of location for FDI. The analysis is conducted using two models: a multicountry model, containing seven industrialized countries; and a multiregion model, consisting of the 11 regions of the UK. Each model attempts to encompass all those locational factors which previous work has shown to be of potential importance. At country level, it is found that market size variables (income and growth), unemployment, level of host country imports and certain policy variables (corporate tax and interest rates) are significant determinants of location. The result of an earlier study that unemployment actually encourages FDI is confirmed; this is perhaps because it proxies labour availability. At regional level, population density, unit labour costs and unemployment (again positive) are the most influential factors.},
-author = {Billington, Nicholas},
-doi = {doi.org/10.1080/000368499324561},
-journal = {Applied Economics},
-number = {3},
-pages = {65--76},
-title = {{The location of foreign direct investment: an empirical analysis}},
-url = {http://www.ingentaconnect.com/content/routledg/raef/1999/00000031/00000001/art00008},
-volume = {31},
-year = {1999}
-}
-@misc{Charney2009,
-author = {Charney, Noah and Record, Sydne},
-title = {{vegetarian: Jost Diversity Measures for Community Data}},
-url = {http://cran.r-project.org/package=vegetarian},
-year = {2009}
-}
-@article{May2011,
-abstract = {We are astonishingly ignorant about how many species are alive on earth today, and even more ignorant about how many we can lose yet still maintain ecosystem services that humanity ultimately depends upon. Mora et al.'s paper is important in offering an imaginative new approach to assessing total species numbers, both on land and in the sea.},
-author = {May, Robert M.},
-doi = {10.1371%2Fjournal.pbio.1001130},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May - 2011 - Why Worry about How Many Species and Their Loss.pdf:pdf},
-journal = {PLoS Biology},
-number = {8},
-pages = {e1001130},
-title = {{Why Worry about How Many Species and Their Loss?}},
-url = {http://dx.doi.org/10.1371{\%}2Fjournal.pbio.1001130},
-volume = {9},
-year = {2011}
-}
-@article{Combes2005,
-abstract = {We develop a methodology to accurately compute transport costs. Based on the real transport network, our measure encompasses the characteristics of infrastructure, vehicle and energy used, as well as labor, insurance, tax and general charges borne by transport carriers. Computed for the 341 French employment areas, road transport shipments andthe period 1978–1998,this new measure is compared to alternative ones such as great circle distance, real distance, or real time. We conclude that these proxies do a very good job in capturing transport costs in cross-section analysis. However, important discrepancies limit the possibility of using them in time series analysis. Moreover, our measure allows us to identify the policies that most impact transport costs.Weshow that transport technology and market structure are responsible for most of the transport cost decrease. Infrastructure improvements only condition the spatial distribution of the gains. Finally, some implications for researchers and regional policy makers are derived.},
-author = {Combes, Pierre-Philippe and Lafourcade, Miren},
-doi = {10.1093/jnlecg/lbh062},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Combes, Lafourcade - 2005 - Transport costs Measures, determinants, and regional policy implications for France.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {3},
-pages = {319--349},
-title = {{Transport costs: Measures, determinants, and regional policy implications for France}},
-url = {https://academic.oup.com/joeg/article-abstract/5/3/319/947001/Transport-costs-measures-determinants-and-regional},
-volume = {5},
-year = {2005}
-}
-@article{Rosenthal2001,
-abstract = {This paper examines the microfoundations of agglomeration economies for U.S. manufacturing industries. Using industries as observations, we regress the Ellison and Glaeser measure of spatial concentration on industry characteristics that proxy for the presence of knowledge spillovers, labor market pooling, input sharing, product shipping costs, and natural advantage. The analysis is conducted separately at the zipcode, county, and state levels. Results indicate that proxies for labor market pooling have the most robust effect, positively influencing agglomeration at all levels of geography. Proxies for knowledge spillovers, in contrast, positively affect agglomeration only at the zipcode level. Reliance on manufactured inputs or natural resources positively affects agglomeration at the state level but has little effect on agglomeration at lower levels of geography. The same is true for the perishability of output, a proxy for product shipping costs.},
-author = {Rosenthal, Stuart S. and Strange, William C.},
-doi = {10.1006/juec.2001.2230},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rosenthal, Strange - 2001 - The Determinants of Agglomeration.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {2},
-pages = {191--229},
-title = {{The Determinants of Agglomeration}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119001922302},
-volume = {50},
-year = {2001}
-}
-@article{Novotny2007,
-abstract = {Recent advances in understanding insect communities in tropical forests have contributed little to our knowledge of large-scale patterns of insect diversity, because incomplete taxonomic knowledge of many tropical species hinders the mapping of their distribution records. This impedes an understanding of global biodiversity patterns and explains why tropical insects are under-represented in conservation biology. Our study of approximately 500 species from three herbivorous guilds feeding on foliage (caterpillars, Lepidoptera), wood (ambrosia beetles, Coleoptera) and fruit (fruitflies, Diptera) found a low rate of change in species composition (beta diversity) across 75,000 square kilometres of contiguous lowland rainforest in Papua New Guinea, as most species were widely distributed. For caterpillars feeding on large plant genera, most species fed on multiple host species, so that even locally restricted plant species did not support endemic herbivores. Large plant genera represented a continuously distributed resource easily colonized by moths and butterflies over hundreds of kilometres. Low beta diversity was also documented in groups with differing host specificity (fruitflies and ambrosia beetles), suggesting that dispersal limitation does not have a substantial role in shaping the distribution of insect species in New Guinea lowland rainforests. Similar patterns of low beta diversity can be expected in other tropical lowland rainforests, as they are typically situated in the extensive low basins of major tropical rivers similar to the Sepik-Ramu region of New Guinea studied here.},
-author = {Novotny, Vojtech and Miller, Scott E. and Hulcr, Jiri and Drew, Richard A. I. and Basset, Yves and Janda, Milan and Setliff, Gregory P. and Darrow, Karolyn and Stewart, Alan J. A. and Auga, John and Isua, Brus and Molem, Kenneth and Manumbor, Markus and Tamtiai, Elvis and Mogia, Martin and Weiblen, George D.},
-doi = {10.1038/nature06021},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Novotny et al. - 2007 - Low beta diversity of herbivorous insects in tropical forests.pdf:pdf},
-journal = {Nature},
-number = {7154},
-pages = {692--5},
-title = {{Low beta diversity of herbivorous insects in tropical forests.}},
-volume = {448},
-year = {2007}
-}
-@article{Gasc2015,
-author = {Gasc, Amandine and Pavoine, Sandrine and Lellouch, L. and Grandcolas, Philippe and Sueur, J{\'{e}}r{\^{o}}me},
-doi = {10.1016/j.biocon.2015.06.018},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gasc et al. - 2015 - Acoustic indices for biodiversity assessments Analyses of bias based on simulated bird assemblages and recommendati.pdf:pdf},
-journal = {Biological Conservation},
-pages = {306--312},
-title = {{Acoustic indices for biodiversity assessments: Analyses of bias based on simulated bird assemblages and recommendations for field surveys}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320715002414},
-volume = {191},
-year = {2015}
-}
-@article{Eaton1982,
-author = {Eaton, B. C. and Lipsey, R. G.},
-doi = {10.2307/2232256},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eaton, Lipsey - 1982 - An Economic Theory of Central Places.pdf:pdf},
-journal = {Economic Journal},
-number = {365},
-pages = {56--72},
-title = {{An Economic Theory of Central Places}},
-url = {https://www.jstor.org/stable/2232256},
-volume = {92},
-year = {1982}
-}
-@article{Rejou-Mechain2011a,
-abstract = {Little is known about the combined impact of habitat filtering and dispersal limitation on species turnover patterns. To gain new insights, we constructed a spatially explicit community model wherein we controlled dispersal distances, the strength of habitat filtering, and the grain of habitat heterogeneity to study the distance decay of several (dis)similarity indices. The impact of habitat filtering is dependent on the ratio between the grain of habitats and the mean dispersal distance. The behavior of (dis)similarity indices varies. First, incidence-based measures of species overlap are less affected by habitat filtering than are abundance-based indices. Second, species identity-based indices, derived from population genetics' F(ST), show interesting capacities to infer dispersal processes under neutrality but are also highly sensitive to habitat filtering. All indices except F(ST)-related indices under neutrality are very sensitive to overall species richness. Hence, community patterns showing contrasted diversity levels should be compared with caution. Partitioning similarity indices within and between habitats appears to be an efficient approach to assess the strength of habitat filtering, and we show that a torus-translation test is powerful for this purpose. We finally highlight the need for further analytical studies to achieve theoretical expectations of similarity decay under dispersal and niche processes.},
-author = {R{\'{e}}jou-M{\'{e}}chain, Maxime and Hardy, Olivier J.},
-doi = {10.1086/659627},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/R{\'{e}}jou-M{\'{e}}chain et al. - 2011 - Spatial aggregation of tropical trees at multiple spatial scales.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/R{\'{e}}jou-M{\'{e}}chain et al. - 2011 - Spatial aggregation of tropical trees at multiple spatial scales (suppl mater).doc:doc},
-journal = {The American naturalist},
-number = {5},
-pages = {589--604},
-title = {{Properties of similarity indices under niche-based and dispersal-based processes in communities.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/21508606},
-volume = {177},
-year = {2011}
-}
-@article{Farquhar1982,
-abstract = {The limitations on carbon dioxide assimilation by plants caused by stomata, particularly when the plant is under stress, are discussed. Mechanisms by which stomatal movement is integrated with photosynthesic requirements are described.},
-author = {Farquhar, G. D. and Sharkey, T. D.},
-doi = {10.1146/annurev.pp.33.060182.001533},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Farquhar, Sharkey - 1982 - Stomatal conductance and photosynthesis.pdf:pdf},
-journal = {Annual Review of Plant Physiology},
-pages = {317--345},
-title = {{Stomatal conductance and photosynthesis}},
-url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.33.060182.001533?journalCode=arplant.1},
-volume = {33},
-year = {1982}
-}
-@article{Connor1979,
-annote = {ArticleType: research-article / Full publication date: Jun., 1979 / Copyright {\^{A}}{\textcopyright} 1979 The University of Chicago Press},
-author = {Connor, Edward F. and McCoy, Earl D.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Connor, McCoy - 1979 - The Statistics and Biology of the Species-Area Relationship.pdf:pdf},
-journal = {The American Naturalist},
-number = {6},
-pages = {791--833},
-title = {{The Statistics and Biology of the Species-Area Relationship}},
-url = {http://www.jstor.org/stable/2460305},
-volume = {113},
-year = {1979}
-}
-@book{Chiu2013,
-address = {Chichester},
-author = {Chiu, Sung Nok and Stoyan, Dietrich and Kendall, W. S. and Mecke, Joseph},
-edition = {3rd Ed.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu et al. - 2013 - Stochastic Geometry and its Applications.pdf:pdf},
-isbn = {9781118658246,1118658248,9781118658253,1118658256,9781118658222,1118658221,0470664819,978-0-470-66481-0,9781299940840,1299940846},
-publisher = {Wiley},
-series = {Wiley Series in Probability and Statistics},
-title = {{Stochastic Geometry and its Applications}},
-year = {2013}
-}
-@article{Shapiro1985,
-abstract = {Models were developed for describing the regular pattern of blue cones in macaque retina. Two functional descriptions were applied to patterns, one based on the cdf of interpoint distances, the other on the cdf of the central angles of Voronoi regions. Disordered triangular and square lattices and hard balls failed to model the blue-cone point pattern. An elastic-ball model was developed whose spatial properties fit well those of the blue-cone pattern. This model employed a hard core and a soft surrounding shell and is proposed as a valid model for the blue-cone pattern.},
-author = {Shapiro, M. B. and Schein, S. J. and de Monasterio, F. M.},
-doi = {10.2307/2288535},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shapiro, Schein, Monasterio - 1985 - Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina.pdf:pdf},
-journal = {Journal of the American Statistical Association},
-number = {392},
-pages = {803--812},
-title = {{Regularity and Structure of the Spatial Pattern of Blue Cones of Macaque Retina}},
-url = {https://www.jstor.org/stable/2288535},
-volume = {80},
-year = {1985}
-}
-@article{Podani2011,
-abstract = {A conceptual framework is proposed to evaluate the relative importance of beta diversity, nestedness and agreement in species richness in presence absence data matrices via partitioning pairwise gamma diversity into additive components. This is achieved by calculating three complementary indices that measure similarity, relative species replacement, and relative richness difference for all pairs of sites, and by displaying the results in a two-dimensional simplex diagram, or ternary plot. By summing two terms at a time, three one-dimensional simplices are derived correspondig to different contrasts: beta diversity versus similarity, species replacement versus nestedness and, finally, richness difference versus richness agreement. The simplex diagrams can be used to interpret underlying data structures by showing departure from randomness towards well-interpretable directions, as demonstrated by artificial and actual examples. In particular, one may appreciate how far data structure deviates from three extreme model situations: perfect nestedness, anti-nestedness and perfect gradient. Throughout the paper, we pay special attention to the measurement and interpetation of beta diversity and nestedness for pairs of sites, because these concepts have been in focus of ecological reseach for decades. The novel method can be used in community ecology, conservation biology, and biogeography, whenever the objective is to recover explanatory ecological processes behind patterns conveyed by presenceabsence data.},
-author = {Podani, J{\'{a}}nos and Schmera, D{\'{e}}nes},
-doi = {10.1111/j.1600-0706.2011.19451.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani, Schmera - 2011 - A new conceptual and methodological framework for exploring and explaining pattern in presence - absence data.pdf:pdf},
-journal = {Oikos},
-number = {11},
-pages = {1625--1638},
-title = {{A new conceptual and methodological framework for exploring and explaining pattern in presence - absence data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2011.19451.x/abstract},
-volume = {120},
-year = {2011}
-}
-@article{Bloom1985,
-abstract = {Our survey of the literature suggests that at least the vegetative growth of plants conforms closely to those theorems of economics that predict how profit should be maximized and resources optimally allocated. Plants do adjust phenology and life history patterns to acquire resources when they are cheap, to store these resources internally and to utilize them when conditions are most favorable for growth (Prediction 1). Plants apparently do continue to produce leaves (and perhaps roots) only until the marginal revenue from this increased production is equal to the marginal cost (Prediction 2). Plants adjust allocation so that their limitation of growth is more nearly equal for all resources (Prediction 3). This theorem describes growth in relation to resource limitations more accurately than does Liebig's law of the minimum (i.e. that only one resource limits growth at any time). Perhaps the most interesting conclusion of this review is that plants adjust physiologically to changes in resource availability to reduce extreme exchange ratios (Prediction 5). Consequently the balance of internal reserves within the plant approaches the proportions that are optimal for growth of most plants. We propose that the economic concepts developed here could provide a useful framework for integrating future studies of plant resource acquisition and allocation.},
-author = {Bloom, Arnold J. and Chapin, F. Stuart III and Mooney, Harold A.},
-doi = {10.1146/annurev.es.16.110185.002051},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bloom, Stuart Chapin, Mooney - 1985 - Resource Limitation in Plants - An Economic Analogy.pdf:pdf},
-journal = {Annual Review of Ecology and Systematics},
-pages = {363--392},
-title = {{Resource Limitation in Plants - An Economic Analogy}},
-url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.es.16.110185.002051?journalCode=ecolsys.1},
-volume = {16},
-year = {1985}
-}
-@article{Bossdorf2000,
-abstract = {The investigation of vegetation pattern and plant association by spatial statistics has become increasingly popular among plant ecologists. Recently, Individual-centered analysis (ICA) has been introduced as a new tool for analysis of multi-species co-occurrence patterns. We tested this new technique by applying it to spatial data from grazed and ungrazed shrub communities in the semi-arid Great Karoo, South Africa. There were substantial but complex and scale-dependent differences in pattern between grazed and ungrazed vegetation. Unpalatable species that increase in abundance in grazed vegetation possibly play a key role in the change of vegetation pattern. At small scales we found indications of aggregation ({\textless} 30 cm) at the ungrazed, but of repulsion (30 - 40 cm) at the grazed site. An additional non-random pattern at 60 - 170 cm at the grazed site was probably due to the clumped distributions of some species on broader scales. We show that the interpretability of ICA results is improved when the actual observed and expected frequencies of species combinations are added to the program output. The main strength of ICA is that it has the potential to detect association patterns that involve more than two species.},
-annote = {326HD
-J VEG SCI},
-author = {Bossdorf, Oliver and Schurr, Frank M. and Schumacher, Jens},
-doi = {10.2307/3236804},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bossdorf, Schurr, Schumacher - 2000 - Spatial patterns of plant association in grazed and ungrazed shrublands in the semi-arid Karoo, So.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {253--258},
-title = {{Spatial patterns of plant association in grazed and ungrazed shrublands in the semi-arid Karoo, South Africa}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236804/full},
-volume = {11},
-year = {2000}
-}
-@article{Basset1999,
-author = {Basset, Y.},
-doi = {doi=10.1.1.452.4871},
-journal = {Ecological Entomology},
-pages = {245--59},
-title = {{Diversity and abundance of insect herbivores on seedlings in a rainforest in Guyana}},
-volume = {24},
-year = {1999}
-}
-@article{Condit1996,
-abstract = {1 Species-accumulation curves for woody plants were calculated in three tropical forests, based on fully mapped 50-ha plots in wet, old-growth forest in Peninsular Malaysia, in moist, old-growth forest in central Panama, and in dry, previously logged forest in southern India. A total of 610 000 stems were identified to species and mapped to {\textless} 1 m accuracy. Mean species number and stem number were calculated in quadrats as small as 5 m x 5 m to as large as I 000 m x 500 m, for a variety of stem sizes above10 mm in diameter. Species-area curves were generated by plotting species number as a function of quadrat size; species-individual curves were generated from the same data, but using stem number as the independent variable rather than area. 2 Species-area curves had different forms for stems of different diameters, but species-individual curves were nearly independent of diameter class. With {\textless} 10000 stems, species-individual curves were concave downward on log-log plots, with curves from different forests diverging, but beyond about 10000 stems, the log-log curves became nearly linear, with all three sites having a similar slope. This indicates an asymptotic difference in richness between forests: the Malaysian site had 2.7 times as many species as Panama, which in turn was 3.3 times as rich as India. 3 Other details of the species-accumulation relationship were remarkably similar between the three sites. Rectangular quadrats had 5-27{\%} more species than square quadrats of the same area, with longer and narrower quadrats increasingly diverse. Random samples of stems drawn from the entire 50ha had 10-30{\%} more species than square quadrats with the same number of stems. At both Pasoh and BCI, but not Mudumalai, species richness was slightly higher among intermediate-sized stems (50--100mm in diameter) than in either smaller or larger sizes. These patterns reflect aggregated distributions of individual species, plus weak density-dependent forces that tend to smooth the species abundance distribution and 'loosen' aggregations as stems grow. 4 The results provide support for the view that within each tree community, many species have their abundance and distribution guided more by random drift than deterministic interactions. The drift model predicts that the species-accumulation curve will have a declining slope on a log-log plot, reaching a slope of 0.1 in about 50 ha. No other model of community structure can make such a precise prediction. 5 The results demonstrate that diversity studies based on different stem diameters can be compared by sampling identical numbers of stems. Moreover, they indicate that stem counts {\textless} 1000 in tropical forests will underestimate the percentage difference in species richness between two diverse sites. Fortunately, standard diversity indices (Fisher's a, Shannon-Wiener) captured diversity differences in small stem samples more effectively than raw species richness, but both were sample size dependent. Two non parametric richness estimators (Chao, jackknife) performed poorly, greatly underestimating true species richness.},
-author = {Condit, Richard and Hubbell, Stephen P. and Lafrankie, James V. and Sukumar, Raman and Manokaran, N. and Foster, Robin B. and Ashton, Peter S.},
-doi = {10.2307/2261477},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Condit et al. - 1996 - Species-Area and Species-Individual Relationships for Tropical Trees A Comparison of Three 50-ha Plots.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {549--562},
-title = {{Species-Area and Species-Individual Relationships for Tropical Trees: A Comparison of Three 50-ha Plots}},
-url = {https://www.jstor.org/stable/2261477?seq=1{\#}page{\_}scan{\_}tab{\_}contents},
-volume = {84},
-year = {1996}
-}
-@article{Grinnell1917,
-abstract = {the CA thrasher has a restricted range...probably due to adaptation to a narrow range of physical conditions.},
-archivePrefix = {arXiv},
-arxivId = {z0063},
-author = {Grinnell, Joseph},
-doi = {10.2307/4072271},
-eprint = {z0063},
-isbn = {00048038},
-issn = {00048038},
-journal = {The Auk},
-number = {4},
-pages = {427--433},
-pmid = {744},
-title = {{The Niche-Relationships of the California Thrasher}},
-url = {http://www.jstor.org/stable/info/10.2307/4072271},
-volume = {34},
-year = {1917}
-}
-@incollection{Warwick2001,
-address = {New York},
-author = {Warwick, R. M. and Clarke, K. R.},
-booktitle = {Oceanography and Marine Biology. An Annual Review.},
-editor = {Gibson, R.N. and Barnes, Margaret and Atkinson, R. J. A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Warwick, Clarke - 1995 - New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress.pdf:pdf},
-pages = {207--232},
-publisher = {Taylor {\&} Francis},
-title = {{Practical Measures of Marine Biodiversity Based on Relatedness of Species}},
-volume = {39},
-year = {2001}
-}
-@book{Wilson1988,
-address = {Washington, D.C.},
-editor = {Wilson, Edward O. and Peter, Frances M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Unknown - 1988 - Biodiversity.pdf:pdf},
-isbn = {9780309567367},
-publisher = {The National Academies Press},
-title = {{Biodiversity}},
-url = {http://www.nap.edu/openbook.php?record{\_}id=989},
-year = {1988}
-}
-@article{Messier2017,
-abstract = {Trait-based approaches have an increasingly dominant role in community ecology. Although trait-based strategy dimensions such as the leaf economic spectrum (LES) have been identified primarily at global-scales, trait variation at the community scale is often interpreted in this context. Here we argue from several lines of evidence that a research priority should be to determine whether global- scale trait relationships hold at more local scales. We review recent literature assessing trait variation at smaller scales, and then present a case study exploring the relationship between the correlation strength of leaf traits and their similarity in variation structure across ecological scales. We find that the correlation strength between pairs of leaf traits does not predict whether the traits respond similarly to different drivers of variation. Instead, correlation strength only sets an upper bound to the dissimilarity in trait variation structure. With moderate correlation strengths, LES traits largely retain the ability to respond independently to different drivers of phenotypic variation at different scales. Recent literature and our results suggest that LES relationships may not hold at local scales. Clarifying under what conditions and at which scales the LES is consistently expressed is necessary for us to make the most of the emerging trait toolbox.},
-author = {Messier, Julie and McGill, Brian J. and Enquist, Brian J. and Lechowicz, Martin J.},
-doi = {10.1111/ecog.02006},
-file = {::},
-isbn = {6503251521},
-issn = {16000587},
-journal = {Ecography},
-number = {6},
-pages = {685--697},
-title = {{Trait variation and integration across scales: is the leaf economic spectrum present at local scales?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02006/abstract},
-volume = {40},
-year = {2017}
-}
-@article{Nakajima2012,
-abstract = {This paper examines location patterns of Japan's manufacturing industries using a unique firm-level dataset on the geographic location of firms. Following the point-pattern approach proposed by Duranton and Overman (2005), we find the following. First, about half of Japan's manufacturing industries can be classified as localized and the number of localized industries is largest for a distance level of 40 km or less. Second, several industries in the textile mill products sector are among the most localized, which is similar to findings for the UK, suggesting that there exist common factors across countries determining the concentration of industrial activities. Third, the distribution of distances between entrant (exiting) firms and remaining firms is, in most industries, not significantly different from a random distribution. These results suggest that most industries in Japan neither become more localized nor more dispersed over time and are in line with similar findings by Duranton and Overman (2008) for the UK. Fourth, a comparison with the service sector indicates that the share of localized industries is higher in manufacturing than in services, although the extent of localization among the most localized manufacturing industries is smaller than that among the most localized service industries, including financial service industries.},
-author = {Nakajima, Kentaro and Saito, Yukiko Umeno and Uesugi, Iichiro},
-doi = {http://dx.doi.org/10.1016/j.jjie.2012.02.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nakajima, Saito, Uesugi - 2012 - Measuring economic localization Evidence from Japanese firm-level data.pdf:pdf},
-journal = {Journal of the Japanese and International Economies},
-number = {2},
-pages = {201--220},
-title = {{Measuring economic localization: Evidence from Japanese firm-level data}},
-url = {http://www.sciencedirect.com/science/article/pii/S0889158312000159},
-volume = {26},
-year = {2012}
-}
-@article{Buckland2011,
-abstract = {The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows ...},
-author = {Buckland, Stephen T. and Studeny, Angelika C. and Magurran, Anne E. and Illian, Janine B. and Newson, Stuart E.},
-doi = {10.1890/ES11-00186.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Buckland et al. - 2011 - The geometric mean of relative abundance indices a biodiversity measure with a difference.pdf:pdf},
-journal = {Ecosphere},
-number = {9},
-pages = {art100},
-title = {{The geometric mean of relative abundance indices: a biodiversity measure with a difference}},
-url = {http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1},
-volume = {2},
-year = {2011}
-}
-@article{Malkinson2003,
-abstract = {Many ecological studies have addressed issues of vegetation spatial patterns in attempts to understand the processes generating them. We investigated changes in ecological processes during succession via the analysis of shrubs' spatial patterns in a system of linear sand dunes, an and ecosystem located in the Negev Desert in Israel during three consecutive years. We hypothesized that spatial patterns change from clustered to regular as succession progresses due to changes in the relative importance of facilitation and competition in this environment. In this ecosystem communities of early successional stages are frequently disturbed by high rates of sand movement, whereas in later successional stages sand stability is high. We mapped in the field individual shrubs on high-resolution aerial photographs, and converted the digital images to a GIS data set. Using Ripley's K-function we analysed spatial patterns at three levels: the single-species level, among species and at the individual level, in three communities characterizing different successional stages. In the early successional communities we found clustered spatial patterns, in comparison with stable habitats where spatial patterns tended to be regular. We argue that these shifts in spatial patterns are indicative of the assumption that in this sand-dune system ecological interactions change from facilitation to competition as succession progresses. Further, we argue that these interactions operate in different spatial scales at the different successional stages, and that the study of these processes should be conducted at the spatial scales specific to each community.},
-annote = {Article
-English
-J VEG SCI
-694ZA},
-author = {Malkinson, D. and Kadmon, R. and Cohen, D.},
-doi = {10.1111/j.1654-1103.2003.tb02146.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Malkinson, Kadmon, Cohen - 2003 - Pattern analysis in successional communities - An approach for studying shifts in ecological interacti.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {213--222},
-title = {{Pattern analysis in successional communities - An approach for studying shifts in ecological interactions}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2003.tb02146.x/abstract},
-volume = {14},
-year = {2003}
-}
-@article{Jost2009a,
-annote = {Times Cited: 7},
-author = {Jost, Lou},
-doi = {10.1111/j.1365-294X.2009.04186.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jost - 2009 - D vs. GST Response to Heller and Siegismund (2009) and Ryman and Leimar (2009).pdf:pdf},
-journal = {Molecular Ecology},
-number = {10},
-pages = {2088--2091},
-title = {{D vs. GST: Response to Heller and Siegismund (2009) and Ryman and Leimar (2009)}},
-volume = {18},
-year = {2009}
-}
-@article{Weithoff2003,
-abstract = {1. This is a discussion of the applicability to the phytoplankton of the concepts of 'plant functional types' (PFTs) and 'functional diversity' (FD), which originated in terrestrial plant ecology. 2. Functional traits driving the performance of phytoplankton species reflect important processes such as growth, sedimentation, grazing losses and nutrient acquisition. 3. This paper presents an objective, mathematical way of assigning PFTs and measuring FD. Ecologists can use this new approach to investigate general hypotheses [e.g. the intermediate disturbance hypothesis (IDH), the insurance hypothesis and synchronicity phenomena] as, for example, in its original formulation the IDH makes its predictions based on FD rather than species diversity.},
-author = {Weithoff, G.},
-doi = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2427.2003.01116.x/abstract},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Weithoff - 2003 - The concepts of 'plant functional types' and 'functional diversity' in lake phytoplankton - a new understanding of phy.pdf:pdf},
-journal = {Freshwater Biology},
-number = {9},
-pages = {1669--1675},
-title = {{The concepts of 'plant functional types' and 'functional diversity' in lake phytoplankton - a new understanding of phytoplankton ecology?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2427.2003.01116.x/abstract},
-volume = {48},
-year = {2003}
-}
-@article{Stoddart1983,
-abstract = {A statistic was designed to compare the observed genotypic diversity of a sample with the expected genotypic diversity calculated from sample gene frequencies, using the assumptions of Hardy-Weinberg equilibria and linkage equi- libria. The relationship of expected genotypic di- versity to the sample size was investigated.},
-author = {Stoddart, James A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoddart - 1983 - A genotypic diversity measure.pdf:pdf},
-journal = {Journal of Heredity},
-pages = {489--490},
-title = {{A genotypic diversity measure}},
-url = {http://jhered.oxfordjournals.org/content/74/6/489.short},
-volume = {74},
-year = {1983}
-}
-@article{Hutchinson1957,
-author = {Hutchinson, George Evelyn},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hutchinson - 1957 - Concluding remarks.pdf:pdf},
-isbn = {0121819639},
-issn = {0927-3042},
-journal = {Cold Spring Harbor Symposia on Quantitative Biology},
-number = {2},
-pages = {415--427},
-title = {{Concluding remarks}},
-volume = {2},
-year = {1957}
-}
-@article{Warton2011,
-abstract = {The arcsine square root transformation has long been standard procedure when analyzing proportional data in ecology, with applications in data sets containing binomial and non-binomial response variables. Here, we argue that the arcsine transform should not be used in either circumstance. For binomial data, logistic regression has greater interpretability and higher power than analyses of transformed data. However, it is important to check the data for additional unexplained variation, i.e., overdispersion, and to account for it via the inclusion of random effects in the model if found. For non-binomial data, the arcsine transform is undesirable on the grounds of interpretability, and because it can produce nonsensical predictions. The logit transformation is proposed as an alternative approach to address these issues. Examples are presented in both cases to illustrate these advantages, comparing various methods of analyzing proportions including untransformed, arcsine- and logit-transformed linear models and logistic regression (with or without random effects). Simulations demonstrate that logistic regression usually provides a gain in power over other methods.},
-author = {Warton, David I. and Hui, Francis K. C.},
-doi = {10.1890/10-0340.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Warton, Hui - 2011 - The arcsine is asinine The analysis of proportions in ecology.pdf:pdf},
-journal = {Ecology},
-number = {1},
-pages = {3--10},
-title = {{The arcsine is asinine: The analysis of proportions in ecology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/10-0340.1/abstract},
-volume = {92},
-year = {2011}
-}
-@article{Sorensen1948,
-address = {K{\o}benhavn},
-author = {S{\o}rensen, T.},
-institution = {Det Kongelige Danske Videnskabernes Selskab},
-journal = {Biologiske Skrifter},
-number = {4},
-pages = {1--34},
-publisher = {I kommission hos E. Munksgaard},
-series = {Biologiske Skrifter},
-title = {{A Method of Establishing Groups of Equal Amplitude in Plant Sociology Based on Similarity of Species Content and Its Application to Analyses of the Vegetation on Danish Commons}},
-url = {http://books.google.co.in/books?id=rpS8GAAACAAJ},
-volume = {5},
-year = {1948}
-}
-@article{Leibold2004,
-abstract = {The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch-dynamic view, the species-sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio-temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.},
-author = {Leibold, Mathew A. and Holyoak, M. and Mouquet, Nicolas and Amarasekare, P. and Chase, Jonathan M. and Hoopes, M. F. and Holt, Robert D. and Shurin, J. B. and Law, Richard and Tilman, David and Loreau, Michel and Gonzalez, A.},
-doi = {10.1111/j.1461-0248.2004.00608.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Leibold et al. - 2004 - The metacommunity concept a framework for multi-scale community ecology.pdf:pdf},
-journal = {Ecology Letters},
-number = {7},
-pages = {601--613},
-title = {{The metacommunity concept: a framework for multi-scale community ecology}},
-url = {http://doi.wiley.com/10.1111/j.1461-0248.2004.00608.x},
-volume = {7},
-year = {2004}
-}
-@article{Loop2015,
-abstract = {Background: Testing for clustering atmultiple rangeswithin a single dataset is a common practice in spatial epidemiology. It is not documented whether this approach has an impact on the type 1 error rate. Methods: We estimated the family-wise error rate (FWE) for the difference in Ripley's K functions test, when testing at an increasing number of ranges at an alpha-level of 0.05. Case and control locationswere generated from a Cox process on a square area the size of the continental US (≈ 3, 000, 000mi2). Two thousandMonte Carlo replicates were used to estimate the FWE with 95{\%} confidence intervalswhen testing for clustering at one range, aswell as 10, 50, and 100 equidistant ranges. Results: The estimated FWE and 95{\%} confidence intervalswhen testing 10, 50, and 100 rangeswere 0.22 (0.20 - 0.24), 0.34 (0.31 - 0.36), and 0.36 (0.34 - 0.38), respectively. Conclusions: Testing for clustering atmultiple rangeswithin a single dataset inflated the FWE above the nominal level of 0.05. Investigators should construct simultaneous critical envelopes (available in spatstat package in R), or use a test statistic that integrates the test statistics fromeach range, as suggested by the creators of the difference in Ripley's K functions test.},
-author = {Loop, Matthew Shane and McClure, Leslie A.},
-doi = {10.1186/1476-072X},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loop, McClure - 2015 - Testing for clustering atmany ranges inflates family-wise error rate (FWE).pdf:pdf},
-journal = {International Journal of Health Geographics},
-number = {4},
-title = {{Testing for clustering at many ranges inflates family-wise error rate (FWE)}},
-url = {https://ij-healthgeographics.biomedcentral.com/articles/10.1186/1476-072X-14-4},
-volume = {14},
-year = {2015}
-}
-@book{Williams1964,
-author = {Williams, Carrington Bonsor},
-booktitle = {Theoretical and Experimental Biology},
-publisher = {Academic Press},
-title = {{Patterns in the balance of nature}},
-url = {http://books.google.com/books?id=VSELAAAAMAAJ},
-year = {1964}
-}
-@book{Ben-Akiva1985,
-address = {Cambridge},
-author = {Ben-Akiva, M. and Lerman, S. R.},
-publisher = {MIT Press},
-title = {{Discrete choice analysis: Theory and application to travel demand}},
-year = {1985}
-}
-@article{Steel2007,
-abstract = {If predictions for species extinctions hold, then the ‘tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as measured by its expected contribution to phylogenetic diversity. Our approach considers all possible scenarios for the set of species that will be extant at some future time, and weights them according to their likelihood under an independent (but not iden- tical) distribution on species extinctions. Although the number of extinction scenarios can typically be very large, we show that there is a simple algorithm that will quickly compute this index. The method is implemented and applied to the prosim- ian primates as a test case, and the associated species ranking is compared to a related measure (the ‘Shapley index'). We describe indices for rooted and unrooted trees, and a modi fi cation that also includes the focal taxon's probability of extinc- tion and which links two complementary approaches to conserving phylogenetic diversity},
-author = {Steel, Mike and Mimoto, Aki and Mooers, Arne {\O}.},
-doi = {10.1111/j.1461-0248.2005.00752.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Steel, Mimoto, Mooers - 2007 - Hedging one's bets quantifying a taxon's expected contribution to future phylogenetic diversity.pdf:pdf},
-journal = {Evolutionary Bioinformatics online},
-pages = {237--244},
-title = {{Hedging one's bets: quantifying a taxon's expected contribution to future phylogenetic diversity}},
-url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684137/},
-volume = {3},
-year = {2007}
-}
-@incollection{Cracraft1983,
-abstract = {Systematic biologists have directed much attention to species concepts because they realize that the origin of taxonomic diversity is the fundamental problem of evolutionary biology. Questions such as, What are the units of evolution? and, How do these units originate? thus continually capture the attention of many. It is probably no exaggeration to say that most believe the “systematic” aspects of the problem have been solved to a greater or lesser extent, whereas the task before us now is to understand the “genetic” and “ecologic” components of differentiation, i. e., those aspects often perceived to constitute the “real mechanisms” of speciation: A study of speciation is, to a considerable extent, a study of the genetics and evolution of reproductive isolating mechanisms (Bush, 1975, p. 339). ... a new mechanistic taxonomy of speciation is needed before population genetics, which deals with evolutionary mechanisms, can be properly integrated with speciation theory; that is, the various modes of speciation should be characterized according to the various forces and genetic mechanisms that underly [sic] the evolution of isolating barriers (Templeton 1980, p. 720).},
-author = {Cracraft, Joel},
-booktitle = {Current Ornithology Volume 1},
-doi = {10.1007/978-1-4615-6781-3_6},
-editor = {Johnston, Richard F.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cracraft - 1983 - Species Concepts and Speciation Analysis.pdf:pdf},
-isbn = {978-1-4615-6783-7},
-pages = {159--187},
-publisher = {Springer US},
-series = {Current Ornithology},
-title = {{Species Concepts and Speciation Analysis}},
-url = {http://dx.doi.org/10.1007/978-1-4615-6781-3{\_}6},
-volume = {1},
-year = {1983}
-}
-@phdthesis{NgoBieng2007,
-address = {Paris, France.},
-author = {{Ngo Bieng}, Marie-Ange},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ngo Bieng - 2007 - Construction de mod{\`{e}}les de structure spatiale permettant de simuler des peuplements virtuels r{\'{e}}alistes. Application a.pdf:pdf},
-publisher = {ENGREF},
-title = {{Construction de mod{\`{e}}les de structure spatiale permettant de simuler des peuplements virtuels r{\'{e}}alistes. Application aux peuplements m{\'{e}}lang{\'{e}}s ch{\^{e}}ne sessile - pin sylvestre de la r{\'{e}}gion Centre.}},
-year = {2007}
-}
-@article{Kenkel1988,
-abstract = {Spatial statistics were used to examine the pattern of self-thinning in a 0.25-ha even-aged (65 yr old), pure stand of jack pine in the boreal forest near Elk Lake, Ontario, Canada. The positions of 459 living and 916 dead trees were recorded, and refined nearest neighbor analysis [G( w)] and second-order spatial statistics [L(t)] were used to examine distributional deviations from both the Poisson expectation and the hypothesis of random mortality. The results indicate that the initial (live + dead, n = 1375) distribution was locally random. By contrast, the distribution of live trees was locally highly regular, while the dead trees were significantly more clumped than random mortality would dictate. It is suggested that the development of a strong regular pattern in the survivors is attributable to differential mortality involving two distinct competitive phases: an early scramble phase involving two-sided competition for soil resources, and a later contest phase involving one-sided competition for light. Analysis of L(t) for the live trees indicated a mean “area of influence” for each individual of an {\~{}} 3.5 m radius, suggesting that trees may compete directly only with their immediate neighbors.},
-author = {Kenkel, N. C.},
-doi = {10.2307/1941257},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kenkel - 1988 - Pattern of Self-Thinning in Jack Pine Testing the Random Mortality Hypothesis.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1017--1024},
-title = {{Pattern of Self-Thinning in Jack Pine: Testing the Random Mortality Hypothesis}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1941257/full},
-volume = {69},
-year = {1988}
-}
-@article{Diggle1990,
-author = {Diggle, Peter J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cuzick, Edwards - 1990 - Spatial Clustering for Inhomogeneous Populations.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {1},
-pages = {101},
-title = {{Discussion of the paper by Cuzick and Edwards}},
-volume = {52},
-year = {1990}
-}
-@article{Crist2003,
-abstract = {Species diversity may be additively partitioned within and among samples (alpha and beta diversity) from hierarchically scaled studies to assess the proportion of the total diversity (gamma) found in different habitats, landscapes, or regions. We developed a statistical approach for testing null hypotheses that observed partitions of species richness or diversity indices differed from those expected by chance, and we illustrate these tests using data from a hierarchical study of forest-canopy beetles. Two null hypotheses were implemented using individual- and sample-based randomization tests to generate null distributions for alpha and beta components of diversity at multiple sampling scales. The two tests differed in their null distributions and power to detect statistically significant diversity components. Individual-based randomization was more powerful at all hierarchical levels and was sensitive to departures between observed and null partitions due to intraspecific aggregation of individuals. Sample-based randomization had less power but still may be useful for determining whether different habitats show a higher degree of differentiation in species diversity compared with random samples from the landscape. Null hypothesis tests provide a basis for inferences on partitions of species richness or diversity indices at multiple sampling levels, thereby increasing our understanding of how a and beta diversity change across spatial scales.},
-annote = {ISI Document Delivery No.: 759ED
-Times Cited: 99
-Cited Reference Count: 48
-UNIV CHICAGO PRESS},
-author = {Crist, Thomas O. and Veech, Joseph A. and Gering, Jon C. and Summerville, Keith S.},
-doi = {10.1086/378901},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Crist et al. - 2003 - Partitioning species diversity across landscapes and regions A hierarchical analysis of alpha, beta, and gamma div.pdf:pdf},
-journal = {The American Naturalist},
-number = {6},
-pages = {734--743},
-title = {{Partitioning species diversity across landscapes and regions: A hierarchical analysis of alpha, beta, and gamma diversity}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/378901},
-volume = {162},
-year = {2003}
-}
-@article{Ruzicka1958,
-abstract = {Document introuvable.},
-author = {Ru{\v{z}}i{\v{c}}ka, M.},
-journal = {Biologia, Bratislava},
-pages = {647--661},
-title = {{Anwendung mathematisch-statisticher Methoden in der Geobotanik (synthetische Bearbeitung von Aufnahmen)}},
-volume = {13},
-year = {1958}
-}
-@techreport{Chessel2003,
-address = {Lyon},
-author = {Chessel, Daniel and Thioulouse, Jean and Dufour, Anne-B{\'{e}}atrice},
-booktitle = {Fiche de Biostatistique},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chessel, Thioulouse, Dufour - 2003 - Introduction {\`{a}} la classification hi{\'{e}}rarchique.pdf:pdf},
-number = {Stage 7},
-publisher = {P{\^{o}}le Bioinformatique Lyonnais},
-title = {{Introduction {\`{a}} la classification hi{\'{e}}rarchique}},
-url = {http://pbil.univ-lyon1.fr/R/pdf/stage7.pdf},
-year = {2003}
-}
-@book{Ramade1984,
-author = {Ramade, F.},
-publisher = {McGraw-Hill},
-title = {{El{\'{e}}ments d'{\'{e}}cologie : Ecologie fondamentale}},
-year = {1984}
-}
-@article{Gagic2015,
-abstract = {Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.},
-author = {Gagic, Vesna and Bartomeus, Ignasi and Jonsson, Tomas and Taylor, Astrid and Winqvist, Camilla and Fischer, Christina and Slade, Eleanor M. and Steffan-Dewenter, Ingolf and Emmerson, Mark and Potts, Simon G and Tscharntke, Teja and Weisser, Wolfgang and Bommarco, Riccardo},
-doi = {10.1098/rspb.2014.2620},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gagic et al. - 2015 - Functional identity and diversity of animals predict ecosystem functioning better than species-based indices.pdf:pdf},
-isbn = {10.1098/rspb.2014.2620},
-issn = {1742-5662},
-journal = {Proceedings of the Royal Society B: Biological Sciences},
-pages = {20142620},
-title = {{Functional identity and diversity of animals predict ecosystem functioning better than species-based indices}},
-url = {http://rspb.royalsocietypublishing.org/content/282/1801/20142620},
-volume = {282},
-year = {2015}
-}
-@article{Greig-Smith1965,
-author = {Greig-Smith, Peter and Chadwick, M. J.},
-doi = {10.2307/2257989},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Greig-Smith, Chadwick - 1965 - Data on pattern within plant communities. III. Acacia capparis semi-desert scrub in the Sudan.pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {465--474},
-title = {{Data on pattern within plant communities. III. Acacia capparis semi-desert scrub in the Sudan}},
-url = {http://www.jstor.org/stable/2257989},
-volume = {53},
-year = {1965}
-}
-@article{Izsak2011,
-abstract = {We introduced two new quadratic entropy indices and performed numerical experimentation on biological data sets to reveal their properties. The difference between two individuals was postulated in both cases on the basis of occurrence probabilities of the species concerned. The new measures summarize a different aspect of community properties than biodiversity indices. They may play a critical role among others in population dynamic models and in the analysis of dominance in ecology. The numerical experimentation was based in part on the characteristics of so-called sensitivity graphs. The graphs related to the new indices are very similar to the opposites of sensitivity graphs of diversity indices, generally used in statistical ecology. Further relations between the new indices and concentration indices were analysed on plot diagrams originating from simulated data. From these analyses, we conclude that the new quadratic entropies are close to concentration measures.},
-author = {Izs{\'{a}}k, J{\'{a}}nos and Pavoine, Sandrine},
-doi = {http://dx.doi.org/10.1016/j.ecolind.2010.07.010},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Izs{\'{a}}k, Pavoine - 2011 - New concentration measures as kinds of the quadratic entropy.pdf:pdf},
-journal = {Ecological Indicators},
-number = {2},
-pages = {540--544},
-title = {{New concentration measures as kinds of the quadratic entropy}},
-url = {http://www.sciencedirect.com/science/article/pii/S1470160X10001330},
-volume = {11},
-year = {2011}
-}
-@article{Cassey2014,
-abstract = {The Ellison and Glaeser (1997) index is an unbiased statistic of industrial localization. Though the expected value of the index is known, ad hoc thresholds are used to interpret the extent of localization. We improve the interpretation of the index by simulating confidence intervals that a practitioner may use for a statistical test. In the data, we find cases whose index value is above the ad hoc threshold that are not statistically significant. We find many cases below the ad hoc threshold that are statistically significant. Our simulation program is freely available and is customizable for specific applications.},
-author = {Cassey, Andrew J. and Smith, Ben O.},
-doi = {10.1016/j.jue.2014.02.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cassey, Smith - 2014 - Simulating confidence for the Ellison–Glaeser index.pdf:pdf},
-journal = {Journal of Urban Economics},
-pages = {85--103},
-title = {{Simulating confidence for the Ellison–Glaeser index}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0094119014000242},
-volume = {81},
-year = {2014}
-}
-@book{Gini1912,
-abstract = {Contributo allo Studio delle Distribuzioni e delle Relazioni Statistiche},
-address = {Bologna},
-author = {Gini, Corrado},
-publisher = {C. Cuppini},
-title = {{Variabilit{\`{a}} e mutabilit{\`{a}}}},
-year = {1912}
-}
-@article{Holmes2002,
-abstract = {This paper shows that plants located in areas where an industry concentrates are larger, on average, than plants in the same industry outside such areas. In some sectors, such as manufacturing, the differences are substantial. The connection between size and concentration is stronger than what we would expect to find if plants were randomly distributed like darts on a dartboard.},
-author = {Holmes, Thomas J. and Stevens, John J.},
-doi = {10.1162/003465302760556495},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Holmes, Stevens - 2002 - Geographic Concentration and Establishment Scale.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {4},
-pages = {682--690},
-title = {{Geographic Concentration and Establishment Scale}},
-url = {http://www.mitpressjournals.org/doi/abs/10.1162/003465302760556495?journalCode=rest},
-volume = {84},
-year = {2002}
-}
-@article{Eber2003,
-abstract = {Plant population biology considers the dynamics of plant modules within stands. However, stands themselves may have considerable regional turnover in space and time. These changes in the number, distribution and size of plant stands generate a dynamic spatial pattern with important implications for the spatial and temporal dynamics of phytophagous insects using these plants as a host. During five successive years we studied the regional distribution and patch dynamics of the creeping thistle Cirsium arvense and the distribution of associated populations of the herbivore Urophora cardui (Diptera: Tephritidae), a specialist stem gall former. The study conducted was in a 15 km(2) heterogeneous, agricultural area in northeastern Bavaria. The distribution of the number of plants per patch was skewed with many more small C. arvense patches than large ones. During the five years of study, there was a 50{\%} increase in the number of C. arvense patches, and a decrease in the mean number of plants per patch (= patch size) to less than half the patch size of the first year. Whilst patch size was randomly distributed in space, patch density showed a consistent, non-random spatial pattern. Patch density was spatially auto-correlated, with areas of high or low patch density having a characteristic dimension of ca. 1 km. Patch size was predictable in time and appeared to be regulated by size dependent processes, with the extinction probability of a patch being negatively correlated with its size. Correlated with the decline of C. arvense patch size during the study, the occupancy and total numbers of the herbivore U. cardui had a marked decrease, suggesting that the regional distribution of the stem gall former is not only influenced by patch number but more importantly by the mean patch size. With decreasing patch sizes, U. cardui was faced with an increasingly dynamic landscape due to higher extinction rates of small patches, although the mean distance between host plant patches decreased.},
-annote = {Article
-English
-J VEG SCI
-694ZA},
-author = {Eber, S. and Brandl, R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Eber, Brandl - 2003 - Regional patch dynamics of Cirsium arvense and possible implications for plant-animal interactions.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {2},
-pages = {259--266},
-title = {{Regional patch dynamics of Cirsium arvense and possible implications for plant-animal interactions}},
-url = {http://www.jstor.org/stable/3236701},
-volume = {14},
-year = {2003}
-}
-@article{Shen2003,
-abstract = {In evaluating the effectiveness of further sampling in species taxonomic surveys, a practical and important problem is predicting the number of new species that would be observed in a second survey, based on data from an initial survey. This problem can also be approached by estimating the corresponding expected number of new species. A. R. Solow and S. Polasky recently proposed a predictor (or estimator), with the form of a sum of many terms, that was derived under the assumption that all unobserved species in the initial sample have equal relative abundances. We show in this paper that the sum- mation can be expressed as only one term.We provide a direct justification for the simplified estimator and connect it to an extrapolation formula based on a special type of species accumulation curve. Using the proposed justification, we show that, for large sample sizes, the estimator is also valid under an alternative condition, i.e., species that are represented the same number of times in the initial sample have equal relative abundances in the community. This condition is statistically justified from a Bayesian approach, although the estimator exhibits moderate negative bias for predicting larger samples in highly hetero- geneous communities. In such situations, we recommend the use of a modified estimator that incorporates a measure of heterogeneity among species abundances. An example using field data from the extant rare vascular plant species patterns in the southern Appalachians is presented to compare the various methods.},
-author = {Shen, Tsung-Jen and Chao, Anne and Lin, Chih-Feng},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shen, Chao, Lin - 2003 - Predicting the number of new species in a further taxonomic sampling.pdf:pdf},
-journal = {Ecology},
-number = {3},
-pages = {798--804},
-title = {{Predicting the number of new species in a further taxonomic sampling}},
-volume = {84},
-year = {2003}
-}
-@article{Zhang2007,
-abstract = {A simple frequentist's justification of Turing's formula, an improvement to Turing's formula by means of reduced bias, a clarification of the relationships among various objects related to Turing's formula, a conservative confidence interval to Turing's target, and a conservative testing procedure using observed rank-frequencies under a hypothesized known infinite-dimensional multinomial distribution are given in this paper. As an example, the authorship of the nine-stanza poem "Shall I Die?" is tested against Shakespeare's canon and statistically significant evidence is found for a difference in word type usage.},
-author = {Zhang, Zhiyi and Huang, Hongwei},
-doi = {10.1080/09296170701514189},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang, Huang - 2007 - Turing's formula revisited.pdf:pdf},
-journal = {Journal of Quantitative Linguistics},
-number = {2-3},
-pages = {222--241},
-title = {{Turing's formula revisited}},
-url = {http://dx.doi.org/10.1080/09296170701514189},
-volume = {14},
-year = {2007}
-}
-@article{Niinemets2006,
-abstract = {Successional replacement of intolerant species by shade tolerators along gap-understorey gradients is commonly associated with increasingly higher low-light carbon acquisition capacities of more tolerant species. This doctrine has recently been challenged because of evidence demonstrating larger leaf dry mass per unit area (M-A), lower photosynthetic capacities and inferior whole plant relative growth rates (RGR) in both high and low irradiance in seedlings of shade-tolerators. However, as the individuals of shade-tolerant species often need to endure canopy shade for many years before gap formation, testing of the carbon gain hypothesis of shade tolerance requires examination of species carbon gain potentials during the entire plant ontogeny. Light vs. M-A relationships throughout ontogeny demonstrate that saplings and canopy individuals of shade tolerators do have lower M-A than intolerant species, and moderately higher photosynthetic capacities in low light, resulting in greater whole plant carbon gain capacities at lower light. The apparent discrepancy between results from studies on seedlings vs. saplings/trees is due to M-A increasing at a faster rate in shade intolerators during ontogeny. A strong positive linkage between seed size and species shade tolerance further implies that shade tolerators have larger initial size, absolute growth rate and survivorship in low light despite their lower RGR. The evidence reviewed collectively suggests that the carbon balance concept of species' successional position is valid for both seedlings and saplings, and that the apparent discrepancies in species rankings on the basis of structural and physiological characteristics are driven by variations in initial size and rate of ontogeny. Analyses of species shade tolerance potentials should therefore consider how any suite of adaptive traits varies with ontogeny.},
-author = {Niinemets, {\"{U}}lo},
-doi = {10.1111/j.1365-2745.2006.01093.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Niinemets - 2006 - The controversy over traits conferring shade-tolerance in trees ontogenetic changes revisited.pdf:pdf},
-journal = {Journal of Ecology},
-number = {2},
-pages = {464--470},
-title = {{The controversy over traits conferring shade-tolerance in trees: ontogenetic changes revisited}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2006.01093.x/abstract},
-volume = {94},
-year = {2006}
-}
-@article{Pavoine2012,
-abstract = {1.Quadratic entropy (QE) was developed as a fundamental function for measuring the diversity within a collection, such as a community, or population, from indices of abundance and distance among categories, such as species or alleles. Based on a literature review in the fields of genetics, ecology and statistics and new developments, I analyse the potential of this function for biodiversity studies. 2.Quadratic entropy was established as a generalisation of well-known diversity indices, and has been widely used in molecular ecology and genetics research. It is now integrated within more general frameworks for analysing functional and phylogenetic diversity in ecology. 3.Quadratic entropy can be maximised by removing categories, and several collections can share the maximum diversity, even with highly distinct compositions. Clarifying these statements, I identify all potential indices of the abundance of the categories that maximise QE. 4.By quantifying changes in diversity when mixing collections together, QE can measure differences among collections. Here, I provide a geometric interpretation of these differences that demonstrates their relevance as classical geometric distances. 5.A critical aspect of these distances is obtained if QE is strictly concave; that is, diversity always strictly increases by mixing distinct collections together. More generally, QE can be used to evaluate the effects of various factors on diversity in a framework designated ANOQE (analysis of QE). Generalising ANOVA (analysis of variance), ANOQE uses QE to measure distances between centroids. 6.Importantly, QE is estimated from sampled data and thus requires estimators. Based on these estimators, tests have been developed to compare levels of diversity. Tests of factor effects are evaluated by parametric, jackknife, bootstrap and permutational approaches. However, the procedures associated with these tests that have been suggested thus far only treat a few factors. 7.There is an urgent need for the development of such approaches in biology to deal with experimental factors, observed population and community structure, and different spatial and temporal scales. Together, QE and the ANOQE procedure are likely to have a critical impact on all scientific disciplines interested in any form of diversity.},
-author = {Pavoine, Sandrine},
-doi = {10.1111/j.2041-210X.2011.00181.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine - 2012 - Clarifying and developing analyses of biodiversity towards a generalisation of current approaches.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {509--518},
-title = {{Clarifying and developing analyses of biodiversity: towards a generalisation of current approaches}},
-url = {http://dx.doi.org/10.1111/j.2041-210X.2011.00181.x},
-volume = {3},
-year = {2012}
-}
-@article{Ripley1976a,
-abstract = {This paper provides a rigorous foundation for the second-order analysis of stationary point processes on general spaces. It illuminates the results of Bartlett on spatial point processes, and covers the point processes of stochastic geometry, including the line and hyperplane processes of Davidson and Krickeberg. The main tool is the decomposition of moment measures pioneered by Krickeberg and Vere-Jones. Finally some practical aspects of the analysis of point processes are discussed.},
-author = {Ripley, Brian D.},
-doi = {10.2307/3212829},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1976 - The Second-Order Analysis of Stationary Point Processes.pdf:pdf},
-journal = {Journal of Applied Probability},
-number = {2},
-pages = {255--266},
-title = {{The Second-Order Analysis of Stationary Point Processes}},
-url = {http://www.jstor.org/stable/3212829},
-volume = {13},
-year = {1976}
-}
-@article{Kemeny2014,
-abstract = {Is specialization good for regional economic development?, Regional Studies. Debates about urban growth and change often centre on specialization. However, arguments linking specialization to metropolitan economic development contain diverse, and sometimes conflicting, claims. Is it better to be highly specialized or diversified? Does specialization refer to the absolute or relative scale of an activity in a region? Does specialization have static or evolutionary effects? This paper investigates these questions in theoretical and empirical terms. By analysing local agglomerations over time, it is found that growing absolute specialization is positively linked to wages, while changes in relative concentration are not significantly associated with wage dynamics},
-author = {Kemeny, Thomas and Storper, Michael},
-doi = {10.1080/00343404.2014.899691},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kemeny, Storper - 2015 - Is Specialization Good for Regional Economic Development.pdf:pdf},
-journal = {Regional Studies},
-number = {6},
-pages = {1003--1018},
-title = {{Is Specialization Good for Regional Economic Development?}},
-url = {http://dx.doi.org/10.1080/00343404.2014.899691},
-volume = {49},
-year = {2015}
-}
-@article{Besag1977a,
-author = {Besag, Julian E.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1977 - Modelling Spatial Patterns.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {2},
-pages = {193--195},
-title = {{Comments on Ripley's paper}},
-volume = {39},
-year = {1977}
-}
-@article{Henderson1974,
-author = {Henderson, J. Vernon},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Henderson - 1974 - The Sizes and Types of Cities.pdf:pdf},
-journal = {The American Economic Review},
-number = {4},
-pages = {640--656},
-title = {{The Sizes and Types of Cities}},
-url = {http://www.jstor.org/stable/1813316},
-volume = {64},
-year = {1974}
-}
-@article{Martin2015,
-abstract = {Over 400 million hectares of tropical forest are currently designated as logging concessions. This practice is an important source of timber, but there are concerns about its long-term sustainability and impacts on biodiversity and carbon storage. However, logging impacts vary widely, making generalisation and, consequently, policy implementation, difficult. Recent syntheses of animal biodiversity have indicated that differences in logging intensity - the volume of wood removed ha-1 - might help to explain some of these disparities. In addition, it has widely been assumed that reduced impact logging (RIL) might minimise some of the negative effects of logging; though in practice, this has rarely been tested. To test the hypothesis that RIL reduces negative impacts of selective logging once intensity is controlled for, we used meta-analyses of selective logging impact studies, focusing specifically on (1) residual tree damage, (2) aboveground biomass and (3) tree species richness. Our results indicate that RIL appears to reduce residual tree damage when compared to conventional methods. However, changes in aboveground biomass were negatively related to logging intensity. Any effect of RIL, independent of logging intensity, was difficult to discern since it was carried out at relatively low intensities. Tree richness appeared to increase at low intensities but decreased at higher intensities and any effect of RIL was difficult to detect. Our results tentatively support the hypothesis that RIL reduces the negative impacts of logging on tree damage, but do not support suggestions that RIL reduces loss of aboveground biomass or tree species richness. However, this lack of support may be a result of the relative paucity of data on the topic. Based on our results, we suggest that better evidence is needed to assess the differences between the impacts of RIL and conventional logging. Studies that consider plot-level differences in logging intensity are required to fill this knowledge gap. In addition, there must be clarification of whether RIL is an inherently low intensity practice so that this can be factored into management.},
-author = {Martin, Philip A. and Newton, Adrian C. and Pfeifer, Marion and Khoo, MinSheng and Bullock, James M.},
-doi = {10.1016/j.foreco.2015.07.010},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Martin et al. - 2015 - Impacts of tropical selective logging on carbon storage and tree species richness A meta-analysis.pdf:pdf},
-journal = {Forest Ecology and Management},
-pages = {224--233},
-title = {{Impacts of tropical selective logging on carbon storage and tree species richness: A meta-analysis}},
-url = {http://dx.doi.org/10.1016/j.foreco.2015.07.010},
-volume = {356},
-year = {2015}
-}
-@article{Rao1982,
-abstract = {Three general methods for obtaining measures of diversity within a population and dissimilarity between populations are discussed. One is based on an intrinsic notion of dissimilarity between individuals and others make use of the concepts of entropy and discrimination. The use of a diversity measure in apportionment of diversity between and within populations is discussed.},
-author = {Rao, C. Radhakrishna},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rao - 1982 - Diversity and dissimilarity coefficients a unified approach.pdf:pdf},
-journal = {Theoretical Population Biology},
-pages = {24--43},
-title = {{Diversity and dissimilarity coefficients: a unified approach}},
-volume = {21},
-year = {1982}
-}
-@incollection{Cowell2000,
-abstract = {This article provides an overview of the key issues in inequality measurement and shows how theoretical concepts are related to practical judgements. The principal axioms of distributional analysis are used to show the social-welfare underpinnings of standard ranking principles and to derive families of inequality indices. Recent developments that focus on income differences and reference income levels are examined.},
-author = {Cowell, Frank},
-booktitle = {Handbook of Income Distribution},
-chapter = {2},
-doi = {10.1016/S0014-2921(81)80003-7},
-editor = {Atkison, Anthony B. and Bourguignon, F},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cowell - 2000 - Measurement of Inequality.pdf:pdf},
-isbn = {0444816313},
-number = {6},
-pages = {87--166},
-publisher = {North Holland},
-title = {{Measurement of Inequality}},
-volume = {1},
-year = {2000}
-}
-@book{Upton1985,
-address = {New York},
-author = {Upton, Graham J G and Fingleton, Bernard},
-booktitle = {Wiley Series in Probability and Mathematical Statistics},
-pages = {1--410},
-publisher = {John Wiley {\&} Sons},
-title = {{Spatial Data Analysis by Example, volume 1: Point Pattern and Quantitative Data}},
-volume = {1},
-year = {1985}
-}
-@article{Pearson1900,
-author = {Pearson, Karl},
-doi = {10.1080/14786440009463897},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pearson - 1900 - On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is.pdf:pdf},
-journal = {Philosophical Magazine Series 5},
-number = {302},
-pages = {157--175},
-title = {{On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling}},
-url = {http://dx.doi.org/10.1080/14786440009463897},
-volume = {50},
-year = {1900}
-}
-@book{Marshall1890,
-address = {London},
-author = {Marshall, A.},
-publisher = {Macmillan},
-title = {{Principle of Economics}},
-year = {1890}
-}
-@article{Izsak2001,
-abstract = {We present a new similarity index, taxonomic similarity (∆S), which can be used to measure $\beta$-diversity. ∆S utilises species presence/absence data, and incorporates both higher taxon richness and evenness concepts. It is derived from the average taxonomic distance (relatedness) of any 2 species from different sites. Therefore ∆S is analogous to taxonomic distinctness recently developed for biodiversity assessment at $\alpha$- and $\gamma$- (landscape or seascape) scales. ∆S is a new index, although its derivation uses a concept similar to the ‘optimal taxonomic mapping statistic' developed independently for quantifying structural redundancy in marine macrobenthos. Using echinoderm data, we show that ∆S exhibits smoother behaviour and is less influenced by species richness, and hence sampling effort, than the widely used Jaccard coefficient of species similarity. We also believe ∆S to be a more intuitive and comprehensive measure of similarity than Jaccard and other conventional indices based solely on species held in common. Taxonomic similarity between sites is computed for echinoderms examined over 3 different spatial scales: local/small-scale ({\textless}10 km), intermediate-scale (10 to 100s km) and province/oceanic-scale (100s to 1000s km). Taxonomic similarity between sites increases progressively with spatial scale, with significantly lower values and higher $\beta$-diversity at small spatial scales. The same pattern is evident for species similarity, using the Jaccard coefficient. Possible explanations for this pattern centre on: (1) the large-scale oceanic area examined (Indo-West Pacific), representing a metapopulation of echinoderms for the 2 other, smaller areas examined within (Pula W{\'{e}}, Sumatra and Lakshadweeps); (2) greater biophysical instability and unpredictability at small spatial scales. Compared with larger spatial scales, these may be characterised by greater likelihood and influence of species migrations and extinctions on a site's total species composition. Hence, species composition may be highly changeable at small scales, leading to high $\beta$-diversity. These findings are based on 1 set of comparative data for 1 faunal group. Any wider conclusions drawn would be premature, although corals may also show greater $\beta$-diversity at small spatial scales. The extent to which patterns observed are evident for other marine species groups is not well known.},
-author = {Izsak, C. and Price, A. R. G.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Izsak, Price - 2001 - Measuring $\beta$-diversity using a taxonomic similarity index , and its relation to spatial scale.pdf:pdf},
-journal = {Marine Ecology Progress Series},
-pages = {69--77},
-title = {{Measuring $\beta$-diversity using a taxonomic similarity index , and its relation to spatial scale}},
-url = {http://www.int-res.com/articles/meps/215/m215p069.pdf},
-volume = {215},
-year = {2001}
-}
-@article{Roderick1999,
-abstract = {1. In this paper we develop a theoretical framework for describing the composition and morphology of leaves on a volumetric basis which is inclusive of both the liquids and internal air space. That framework is then used to link the composition and morphology with the function of leaves. 2. Leaves are segmented into a functional scheme named a-u-s-V lair space-solution-structure-volume basis) and a measurement scheme named a-q-d-M lair space-liquid-dry matter-Mass basis). Measurements of mass, liquid mass, volume and fractional air space are necessary to (partially) link the two schemes. 3. The liquid content of leaves can be used to infer the mode of mechanical support and, hence, the likely values of air space, solution and structure. For example, if a leaf has a high liquid content, then it cannot have a large volumetric fraction of structure (which is largely made of dry matter) and is unlikely to have large internal air spaces. 4. Based on measurements of individual leaf components, the specific gravity of the non-gaseous fraction in leaves would usually be in the range 1-1.3. Consequently, the specific gravity of leaves would be most sensitive to variation in fractional air space. 5. For the dimensions typical of most leaves, the surface area to volume ratio of a leaf is determined by leaf thickness (or diameter). 6. Leaf design is considered in terms of light interception and gas exchange. The requirements for each are essentially incompatible and lead to a trade-off on leaf thickness. However, that relationship is complicated because Variation in fractional air space can potentially lead to broad optima for gas exchange at any given leaf thickness. 7. The theoretical predictions have not been assessed owing to a lack of measurements of leaf density, fractional air space and Liquid content. However, published data were used to develop the following hypotheses: (1) the mass of nitrogen per unit mass of liquid is relatively constant within leaves; (2) the surface area to volume ratio of leaves is proportional to leaf liquid content. These hypotheses are tested in a subsequent paper.},
-author = {Roderick, M. L. and Berry, S. L. and Noble, I. R. and Farquhar, G. D.},
-doi = {10.1046/j.1365-2435.1999.00368.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roderick et al. - 1999 - A theoretical approach to linking the composition and morphology with the function of leaves.pdf:pdf},
-journal = {Functional Ecology},
-number = {5},
-pages = {683--695},
-title = {{A theoretical approach to linking the composition and morphology with the function of leaves}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2435.1999.00368.x/abstract},
-volume = {13},
-year = {1999}
-}
-@article{Loehle1990,
-abstract = {This paper proposes strategies for promoting scientific creativity. After discussing the importance of selecting the right problem or question to investigate, tbe author examines ways of reducing blocks to creativity. He also advises against beoming an expert in a single, narrow field. The value of unhurried, undirected thinking, and the benefits of activities that give rise to reflective thought-such as walking-are also discussed.},
-author = {Loehle, C. S.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loehle - 1990 - A guide to increased creativity in research - inspiration or perspiration.pdf:pdf},
-journal = {Bioscience},
-number = {2},
-pages = {123--129},
-title = {{A guide to increased creativity in research - inspiration or perspiration?}},
-url = {http://www.garfield.library.upenn.edu/essays/v13p240y1990.pdf},
-volume = {40},
-year = {1990}
-}
-@article{Volkov2005,
-abstract = {The recurrent patterns in the commonness and rarity of species in ecological communities - the relative species abundance - have puzzled ecologists for more than half a century(1,2). Here we show that the framework of the current neutral theory in ecology(3 - 10) can easily be generalized to incorporate symmetric density dependence(11 - 14). We can calculate precisely the strength of the rare- species advantage that is needed to explain a given RSA distribution. Previously, we demonstrated that a mechanism of dispersal limitation also fits RSA data well(3,4). Here we compare fits of the dispersal and density- dependence mechanisms for empirical RSA data on tree species in six New and Old World tropical forests and show that both mechanisms offer sufficient and independent explanations. We suggest that RSA data cannot by themselves be used to discriminate among these explanations of RSA patterns(15) - empirical studies will be required to determine whether RSA patterns are due to one or the other mechanism, or to some combination of both.},
-author = {Volkov, Igor and Banavar, Jayanth R. and He, Fangliang and Hubbell, Stephen P. and Maritan, Amos},
-doi = {doi:10.1038/nature04030},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Volkov et al. - 2005 - Density dependence explains tree species abundance and diversity in tropical forests.pdf:pdf},
-journal = {Nature},
-number = {7068},
-pages = {658--661},
-title = {{Density dependence explains tree species abundance and diversity in tropical forests}},
-url = {http://www.nature.com/nature/journal/v438/n7068/abs/nature04030.html},
-volume = {438},
-year = {2005}
-}
-@article{Wright1931,
-author = {Wright, Sewall},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wright - 1931 - Evolution in Mendelian Populations.pdf:pdf},
-journal = {Genetics},
-number = {2},
-pages = {97--159},
-title = {{Evolution in Mendelian Populations}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1201091{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {16},
-year = {1931}
-}
-@article{Clark2016,
-abstract = {Trait analysis aims to understand relationships between traits, species di- versity, and the environment. Current methods could benefit from a model- based proba- bilistic framework that accommodates covariance between traits and quantifies contributions from inherent trait syndromes, species interactions, and responses to the environment. I develop a model- based approach that separates these effects on trait diversity. Application to USDA Forest Inventory and Analysis (FIA) data in the eastern United States demon- strates an apparent paradox, that the analysis of species better explains and predicts traits than does direct analysis of the traits themselves; trait data contain less, not more, infor- mation than species on environmental responses. Whereas variation in some traits is dom- inated by inherent syndromes (tendency for certain traits to be associated with others within an individual and species), others are strongly controlled by variation in species diversity. There is substantial variation in environmental control on trait patterns, between traits and regionally. In terms of environmental response traits do not aggregate into defined plant functional types, as would be desirable for models.},
-author = {Clark, James S.},
-doi = {10.1002/ecy.1453},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clark - 2016 - Why species tell more about traits than traits about species Predictive analysis.pdf:pdf},
-isbn = {0012-9658},
-issn = {00129658},
-journal = {Ecology},
-number = {8},
-pages = {1979--1993},
-title = {{Why species tell more about traits than traits about species: Predictive analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/ecy.1453/abstract},
-volume = {97},
-year = {2016}
-}
-@article{Gower1986,
-abstract = {We assemble here properties of certain dissimilarity coefficients and are specially concerned with their metric and Euclidean status. No attempt is made to be exhaustive as far as coefficients are concerned, but cer- tain mathematical results that we have found useful are presented and should help establish similar properties for other coefficients. The response to different types of data is investigated, leading to guidance on the choice of an appropriate coefficient.},
-author = {Gower, J. C. and Legendre, Pierre},
-doi = {10.1007/BF01896809},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gower, Legendre - 1986 - Metric and Euclidean properties of dissimilarity coefficients.pdf:pdf},
-journal = {Journal of classification},
-pages = {5--48},
-title = {{Metric and Euclidean properties of dissimilarity coefficients}},
-url = {http://link.springer.com/article/10.1007/BF01896809},
-volume = {48},
-year = {1986}
-}
-@article{Jones1986,
-abstract = {We respond to the preceding article by Perry (J. Econ. Entomol. 79: 1149–1155) concerning the subject of hypothesis testing and meaningful presentation of statistical analyses. We agree with Perry that indiscriminate use of statistical hypothesis testing should be discouraged. We also address and refute reasons often given to support continued emphasis on hypothesis testing. We conclude that biologists should take the responsibility for evaluating whether or not the magnitude of the difference between population parameters or treatment effects is biologically important, instead of merely testing for whether such a difference exists. We recommend that authors display the estimate of the difference and the confidence limit for this difference. These statistics, along with the standard error, contain the most information: their presentation provides the clearest and most meaningful format of the statistical analyses.},
-author = {Jones, Davy and Matloff, Norman},
-doi = {10.1093/jee/79.5.1156},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jones, Matloff - 1986 - Statistical Hypothesis Testing in Biology A Contradiction in Terms.pdf:pdf},
-journal = {Journal of Economic Entomology},
-number = {5},
-pages = {1156--1160},
-title = {{Statistical Hypothesis Testing in Biology: A Contradiction in Terms}},
-url = {https://academic.oup.com/jee/article-abstract/79/5/1156/881872/Statistical-Hypothesis-Testing-in-Biology-A?redirectedFrom=fulltext},
-volume = {79},
-year = {1986}
-}
-@article{Meine2006,
-abstract = {Conservation biology emerged in the mid-1980s, drawing on established disciplines and integrating them in pursuit of a coherent goal: the protection and perpetuation of the Earth's biological diversity. Opportunistic in its borrowing and application of knowledge, conservation biology had its roots within the established biological sciences and resource management disciplines but has continually incorporated insights from the empirical experience of resource managers, from the social sciences and humanities, and from diverse cultural sources. The Society for Conservation Biology (SCB) has represented the field's core constituency, while expanding that constituency in keeping with the field's integrative spirit. Conservation Biology has served as SCB's flagship publication, promoting research, dialog, debate, and application of the field's essential concepts. Over the last 20 years the field, SCB, and the journal have evolved to meet changing conservation needs, to explore gaps in our knowledge base, to incorporate new information from related fields, to build professional capacity, and to provide expanded opportunities for international participation. In turn, the field, SCB, and journal have prompted change in related fields, organizations, and publications. In its dedication to advancing the scientific foundations of biodiversity conservation and placing that science at the service of society in a world whose variety, wildness, and beauty we care for conservation biology represents both a continuation and radical reconfiguration of the traditional relationship between science and conservation.},
-author = {Meine, Curt and Soul{\'{e}}, Michael and Noss, Reed F.},
-doi = {10.1111/j.1523-1739.2006.00449.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Meine, Soul{\'{e}}, Noss - 2006 - A mission-driven discipline The growth of conservation biology.pdf:pdf},
-journal = {Conservation Biology},
-number = {3},
-pages = {631--651},
-title = {{"A mission-driven discipline": The growth of conservation biology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2006.00449.x/full},
-volume = {20},
-year = {2006}
-}
-@article{Kang2009,
-abstract = {Although spatial concentration is understood as the premise of agglomeration economies, it hardly observes the changing aspect of externalities. Based on previous studies in which space–time clustering was observed during the initial stage of the product life cycle and sudden changes of historic accident and discovery, the study hypothesizes that space–time clustering better represents the occurring agglomeration economies than spatial concentration alone. For the empirical test, two methods, the space–time K-function and Kulldorff's scan statistic, were applied using the ES-202 data of the Columbus MSA. The study discovered that knowledge-based industries represent the agglomeration process due to the product life cycle and sudden change, and that restructuring of industries, from traditional manufacturing industries to knowledge-based industries, is taking place in the study area. In addition, using the space–time K-function, the study identified the threshold of space–time clustering in which the agglomeration process is taking place.},
-annote = {10.1007/s00168-009-0303-x},
-author = {Kang, Hoje},
-doi = {10.1007/s00168-009-0303-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kang - 2009 - Detecting agglomeration processes using space–time clustering analyses.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {2},
-pages = {291--311},
-title = {{Detecting agglomeration processes using space–time clustering analyses}},
-url = {http://dx.doi.org/10.1007/s00168-009-0303-x},
-volume = {45},
-year = {2010}
-}
-@article{Diggle1979,
-abstract = {The paper discusses the objectives of spatial point pattern analysis, with particular reference to the distinction between mapped and sampled data. For the former case, available models are reviewed briefly, the role of preliminary testing is discussed and a procedure for fitting a parametric model is outlined. A simulation study of several tests of spatial randomness is intended to provide some insight into the suitability for model-fitting of various summary descriptions of a mapped pattern. Two examples illustrate the use of the statistical techniques. Some problem areas which merit further investigation are identified.},
-author = {Diggle, Peter J.},
-doi = {10.2307/2529938},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Diggle - 1978 - On Parameter Estimation for Spatial Point Processes.pdf:pdf},
-journal = {Biometrics},
-number = {1},
-pages = {87--101},
-title = {{On parameter estimation and goodness-of-fit testing for spatial point patterns}},
-url = {https://www.jstor.org/stable/2529938},
-volume = {35},
-year = {1979}
-}
-@article{Balmford1996a,
-abstract = {Attempts to identify priority sites for conserving biodiversity are greatly hampered by a lack of good data on species' distributions. R ecent work suggests one promising solution might be to use higher-level taxa (such as genera or families) which might be more easily surveyed, yet nevertheless still act as reliable surrogates for patterns of species richness. But evidence justifying this approach comes mostly from temperate datasets or inventories over enormous areas, and a number of concerns remain unanswered about the use of higher-taxon richness for identifying key conservation sites in the tropics, where most diversity occurs. Here in the first of two papers addressing these points, we explored congruence between species and higher-taxon richness across protected areas in lndo-Malaya and the Pacific rim. Our results support the use of the higher-taxon approach in guiding tropical conservation, but with certain reservations. In all three groups examined, higher-taxon richness was quite closely related to species number. However, the precision with which absolute species richness of reserves could be predicted from higher-taxon richness was often surprisingly low, particularly for rich sites where surveying higher taxa rather than species would save most time. The performance of higher taxa as surrogates also dropped sharply with increasing taxonomic rank, resulting in a trade-off between time saved by high-level surveys and the value of those surveys. Lastly, we found that species richness within individual higher taxa was potentially as powerful an indicator of the overall species diversity of a site as the number of higher taxa it contained.},
-author = {Balmford, Andrew and Green, M. J. B. and Murray, M. G.},
-doi = {10.1098/rspb.1996.0186},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Balmford, Green, Murray - 1996 - Using higher-taxon richness as a surrogate for species richness I. Regional tests.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-pages = {1267--1274},
-title = {{Using higher-taxon richness as a surrogate for species richness: I. Regional tests}},
-url = {http://rspb.royalsocietypublishing.org/content/263/1375/1267},
-volume = {263},
-year = {1996}
-}
-@article{Stys2015,
-abstract = {We generalize the Point information gain (PIG) and derived quantities, i.e. Point information entropy (PIE) and Point information entropy density (PIED), for the case of R{\'{e}}nyi entropy and simulate the behavior of PIG for typical distributions. We also use these methods for the analysis of multidimensional datasets. We demonstrate the main properties of PIE/PIED spectra for the real data on the example of several images, and discuss possible further utilization in other fields of data processing.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1501.0289},
-author = {{\v{S}}tys, Dalibor and Korbel, Jan and Rycht{\'{a}}rikov{\'{a}}, Renata and Soloviov, Dmytro and C{\'{i}}sař, Petr and Urban, Jan},
-eprint = {arXiv:1501.0289},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/{\v{S}}tys et al. - 2015 - Point information gain , point information gain entropy and point information gain entropy density as measures of s.pdf:pdf},
-journal = {arXiv},
-number = {v2},
-title = {{Point information gain , point information gain entropy and point information gain entropy density as measures of semantic and syntactic information of multidimensional discrete phenomena}},
-url = {https://arxiv.org/abs/1501.02891},
-volume = {1501.02891},
-year = {2015}
-}
-@inproceedings{Scime2015,
-author = {Scime, Anthony},
-booktitle = {Proceedings of Informing Science {\&} IT Education Conference (InSITE)},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Scime - 2015 - A Simple Measure of Diversity.pdf:pdf},
-pages = {367--383},
-title = {{A Simple Measure of Diversity}},
-year = {2015}
-}
-@misc{Cao2014,
-author = {Cao, Lijuan and Grabchak, Michael},
-title = {{EntropyEstimation: Estimation of Entropy and Related Quantities}},
-url = {http://cran.r-project.org/package=EntropyEstimation},
-year = {2014}
-}
-@article{Chiu2007,
-abstract = {Using Ripley's K-function in testing spatial randomness, Koen's estimated critical values deviated notably from Ripley's approximation formula; the former, however, came from an incorrect algorithm. This paper reports newestimates, which agree very well with Ripley's approximation and recommends that the approximation formula can be used instead of Monte-Carlo tests.},
-author = {Chiu, Sung Nok},
-doi = {10.1080/10629360600989147},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chiu - 2007 - Correction to Koen's critical values in testing spatial randomness.pdf:pdf},
-journal = {Journal of Statistical Computation and Simulation},
-number = {11-12},
-pages = {1001--1004},
-title = {{Correction to Koen's critical values in testing spatial randomness}},
-volume = {77},
-year = {2007}
-}
-@article{Hill1973,
-author = {Hill, M. O.},
-doi = {10.2307/1934352},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hill - 1973 - Diversity and Evenness A Unifying Notation and Its Consequences.pdf:pdf},
-journal = {Ecology},
-number = {2},
-pages = {427--432},
-title = {{Diversity and Evenness: A Unifying Notation and Its Consequences}},
-url = {http://www.esajournals.org/doi/abs/10.2307/1934352},
-volume = {54},
-year = {1973}
-}
-@article{Feret2014,
-abstract = {There is a growing need for operational biodiversity mapping methods to quantify and to assess the impact of climate change, habitat alteration, and human activity on ecosystem composition and function. Here, we present an original method for the estimation of a- and b-diversity of tropical forests based on high-fidelity imaging spectroscopy. We acquired imagery over high-diversity Amazonian tropical forest landscapes in Peru with the Carnegie Airborne Observatory and developed an unsupervised method to estimate the Shannon index (H0) and variations in species composition using Bray-Curtis dissimilarity (BC) and nonmetric multidimensional scaling (NMDS). An extensive field plot network was used for the validation of remotely sensed a- and b-diversity. Airborne maps of H0 were highly correlated with field a-diversity estimates (r¼0.86), and BC was estimated with demonstrable accuracy (r¼0.61–0.76). Our findings are the first direct and spatially explicit remotely sensed estimates of a- and b-diversity of humid tropical forests, paving the way for new applications using airborne and space-based imaging spectroscopy.},
-author = {F{\'{e}}ret, Jean-Baptiste and Asner, Gregory P.},
-doi = {10.1890/13-1824.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/F{\'{e}}ret, Asner - 2014 - Mapping tropical forest canopy diversity using high-fidelity imaging spectroscopy.pdf:pdf},
-journal = {Ecological Applications},
-number = {6},
-pages = {1289--1296},
-title = {{Mapping tropical forest canopy diversity using high-fidelity imaging spectroscopy}},
-url = {http://www.esajournals.org/doi/abs/10.1890/13-1824.1},
-volume = {24},
-year = {2014}
-}
-@article{Kenkel1993,
-abstract = {I examined spatial patterns of two populations of the clonal herb Aralia nudicaulis for evidence of spatial inhibition among neighboring ramets. Second-order spatial analysis revealed that ramet patterns of both populations were regular at local spatial scales, a result consistent with the proposition that localized, inter-ramet interactions are important in reducing spatial overlap. Localized ramet interactions suggest Markovian dependence, which is defined when an event (e.g., occurrence of a ramet) at X is dependent solely on the existence or otherwise of an event within a distance d of X. Evidence of Markovian dependence in the populations was tested by fitting Markov point-process models to the observed ramet patterns. The populations conformed well to the Markov model, the results indicating that both ramet spatial patterns were Markov of range d = 18 cm. This inhibition distance corresponds closely to the mean horizontal radius of an A. nudicaulis ramet, indicating that interactions occur at the spatial scale of the individual. I suggest that a likely mechanism for the development of locally regular spatial patterns in these populations is inter-ramet competition for a limiting resource, probably light.},
-author = {Kenkel, N. C.},
-doi = {10.2307/1939928},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kenkel - 1993 - Modeling Markovian Dependence in Populations of Aralia Nudicaulis.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1700--1706},
-title = {{Modeling Markovian Dependence in Populations of Aralia Nudicaulis}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1939928/full},
-volume = {74},
-year = {1993}
-}
-@article{Hooper2005,
-abstract = {Humans are altering the composition of biological communities through a variety of activities that increase rates of species invasions and species extinctions, at all scales, from local to global. These changes in components of the Earth's biodiversity cause concern for ethical and aesthetic reasons, but they also have a strong potential to alter ecosystem properties and the goods and services they provide to humanity. Ecological experiments, observations, and theoretical developments show that ecosystem properties depend greatly on biodiversity in terms of the functional characteristics of organisms present in the ecosystem and the distribution and abundance of those organisms over space and time. Species effects act in concert with the effects of climate, resource availability, and disturbance regimes in influencing ecosystem properties. Human activities can modify all of the above factors; here we focus on modification of these biotic controls. The scientific community has come to a broad consensus on many aspects of the relationship between biodiversity and ecosystem functioning, including many points relevant to management of ecosystems. Further progress will require integration of knowledge about biotic and abiotic controls on ecosystem properties, how ecological communities are structured, and the forces driving species extinctions and invasions. To strengthen links to policy and management, we also need to integrate our ecological knowledge with understanding of the social and economic constraints of potential management practices. Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain. Based on our review of the scientific literature, we are certain of the following conclusions: 1)Species' functional characteristics strongly influence ecosystem properties. Functional characteristics operate in a variety of contexts, including effects of dominant species, keystone species', ecological engineers, and interactions among species (e.g., competition, facilitation, mutualism, disease, and predation). Relative abundance alone is not always a good predictor of the ecosystem-level importance of a species, as even relatively rare species (e.g., a keystone predator) can strongly influence pathways of energy and material flows. 2) Alteration of biota in ecosystems via species invasions and extinctions caused by human activities has altered ecosystem goods and services in many well-documented cases. Many of these changes are difficult, expensive, or impossible to reverse or fix with technological solutions. 3) The effects of species loss or changes in composition, and the mechanisms by which the effects manifest themselves, can differ among ecosystem properties, ecosystem types, and pathways of potential community change. 4) Some ecosystem properties are initially insensitive to species loss because (a) ecosystems may have multiple species that carry out similar functional roles, (b) some species may contribute relatively little to ecosystem properties, or (c) properties may be primarily controlled by abiotic environmental conditions. 5) More species are needed to insure a stable supply of ecosystem goods and services as spatial and temporal variability increases, which typically occurs as longer time periods and larger areas are considered. We have high confidence in the following conclusions: 1) Certain combinations of species are complementary in their patterns of resource use and can increase average rates of productivity and nutrient retention. At the same time, environmental conditions can influence the importance of complementarity in structuring communities. Identification of which and how many species act in a complementary way in complex communities is just beginning. 2) Susceptibility to invasion by exotic species is strongly influenced by species composition and, under similar environmental conditions, generally decreases with increasing species richness. However, several other factors, such as propagule pressure, disturbance regime, and resource availability also strongly influence invasion success and often override effects of species richness in comparisons across different sites or ecosystems. 3) Having a range of species that respond differently to different environmental perturbations can stabilize ecosystem process rates in response to disturbances and variation in abiotic conditions. Using practices that maintain a diversity of organisms of different functional effect and functional response types will help preserve a range of management options. Uncertainties remain and further research is necessary in the following areas: 1) Further resolution of the relationships among taxonomic diversity, functional diversity, and community structure is important for identifying mechanisms of biodiversity effects. 2) Multiple trophic levels are common to ecosystems but have been understudied in biodiversity/ecosystem functioning research. The response of ecosystem properties to varying composition and diversity of consumer organisms is much more complex than responses seen in experiments that vary only the diversity of primary producers. 3) Theoretical work on stability has outpaced experimental, work, especially field research. We need long-term experiments to be able to assess temporal stability, as well as experimental perturbations to assess response to and recovery from a variety of disturbances. Design and analysis of such experiments must account for several factors that covary with species diversity. 4) Because biodiversity both responds to and influences ecosystem properties, understanding the feedbacks involved is necessary to integrate results from experimental communities with patterns seen at broader scales. Likely patterns of extinction and invasion need to be linked to different drivers of global change, the forces that structure communities, and controls on ecosystem properties for the development of effective management and conservation strategies. 5) This paper focuses primarily on terrestrial systems, with some coverage of freshwater systems, because that is where most empirical and theoretical study has focused. While the fundamental principles described here should apply to marine systems, further study of that realm is necessary. Despite some uncertainties about the mechanisms and circumstances under which diversity influences ecosystem properties, incorporating diversity effects into policy and management is essential, especially in making decisions involving large temporal and spatial scales. Sacrificing those aspects of ecosystems that are difficult or impossible to reconstruct, such as diversity, simply because we are not yet certain about the extent and mechanisms by which they affect ecosystem properties, will restrict future management options even further. It is incumbent upon ecologists to communicate this need, and the values that can derive from such a perspective, to those charged with economic and policy decision-making.},
-author = {Hooper, David U. and Chapin, F. Stuart III and Ewel, J. J. and Hector, Andrew and Inchausti, P. and Lavorel, Sandra and Lawton, John H. and Lodge, D. M. and Loreau, Michel and Naeem, Shahid and Schmid, Bernhard and Setala, H. and Symstad, A. J. and Vandermeer, J. and Wardle, David A.},
-doi = {10.1890/04-0922},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hooper, Chapin III, Ewel - 2005 - Effects of biodiversity on ecosystem functioning a consensus of current knowledge.pdf:pdf},
-journal = {Ecological Monographs},
-number = {1},
-pages = {3--35},
-title = {{Effects of biodiversity on ecosystem functioning: A consensus of current knowledge}},
-url = {http://www.esajournals.org/doi/abs/10.1890/04-0922},
-volume = {75},
-year = {2005}
-}
-@article{Ricotta2012b,
-abstract = {1. Recently a number of rarefaction curves including information on species' functional traits were proposed for those measures of functional diversity that monotonically increase with species richness. 2. Building on these methods, in this paper, we propose a functional rarefaction curve for species abundance data that is obtained using the classical diversity decomposition of the Rao quadratic diversity into alpha, beta and gamma diversity. 3. The proposed abundance-based functional rarefaction is illustrated with one dedicated case study in sand dune communities in Italy. 4. Although we put emphasis on functional diversity only, because of its mathematical generality, the proposed method can be extended to virtually any abundance-weighted concave measure for comparing diversityamong habitats sampled with different effort.},
-author = {Ricotta, Carlo and Pavoine, Sandrine and Bacaro, Giovanni and Acosta, Alicia T.R.},
-doi = {10.1111/j.2041-210X.2011.00178.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta et al. - 2012 - Functional rarefaction for species abundance data.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {519--525},
-title = {{Functional rarefaction for species abundance data}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00178.x/abstract},
-volume = {3},
-year = {2012}
-}
-@article{Sobral2016,
-abstract = {The ratio of species extinctions to introductions has been comparable for many insular assem- blages, suggesting that introductions could have ‘compensated' for extinctions. However, the capacity for introduced species to replace ecological roles and evolutionary history lost following extinction is unclear. We investigated changes in bird functional and phylogenetic diversity in the wake of extinctions and introductions across a sample of 32 islands worldwide. We found that extinct and introduced species have comparable functional and phylogenetic alpha diversity. How- ever, this was distributed at different positions in functional space and in the phylogeny, indicat- ing a ‘false compensation'. Introduced and extinct species did not have equivalent functional roles nor belong to similar lineages. This makes it unlikely that novel island biotas composed of intro- duced taxa will be able to maintain ecological roles and represent the evolutionary histories of pre-disturbance assemblages and highlights the importance of evaluating changes in alpha and beta diversity concurrently.},
-author = {Sobral, Fernando L. and Lees, Alexander C. and Cianciaruso, Marcus V.},
-doi = {10.1111/ele.12646},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sobral, Lees, Cianciaruso - 2016 - Introductions do not compensate for functional and phylogenetic losses following extinctions in insul.pdf:pdf},
-journal = {Ecology Letters},
-number = {9},
-pages = {1091--1100},
-title = {{Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12646/full},
-volume = {19},
-year = {2016}
-}
-@article{Solow1994,
-abstract = {The diversity of a set of species refers to the joint dissimilarity of the species in the set. This paper discusses the measurement of diversity from the set of pairwise distances between the species in the set. A measure called the effective number of species is developed from a non-parametric probability inequality and is shown to have a simple interpretation in terms of comparing linear experiments.},
-author = {Solow, Andrew R. and Polasky, Stephen},
-doi = {10.1007/BF02426650},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Solow, Polasky - 1994 - Measuring biological diversity.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {2},
-pages = {95--103},
-title = {{Measuring biological diversity}},
-url = {http://link.springer.com/10.1007/BF02426650},
-volume = {1},
-year = {1994}
-}
-@article{Anderson2001,
-abstract = {Hypothesis-testing methods for multivariate data are needed to make rigorous probability statements about the effects of factors and their interactions in experiments. Analysis of variance is particularly powerful for the analysis of univariate data. The traditional multivariate analogues, however, are too stringent in their assumptions for most ecological multivariate data sets. Non-parametric methods, based on permutation tests, are preferable. This paper describes a new non-parametric method for multivariate analysis of variance, after McArdle and Anderson (in press). It is given here, with several applications in ecology, to provide an alternative and perhaps more intuitive formulation for ANOVA (based on sums of squared distances) to complement the description pro- vided by McArdle and Anderson (in press) for the analysis of any linear model. It is an improvement on previous non-parametric methods because it allows a direct additive partitioning of variation for complex models. It does this while maintaining the flexibility and lack of formal assumptions of other non-parametric methods. The test- statistic is a multivariate analogue to Fisher's F-ratio and is calculated directly from any symmetric distance or dissimilarity matrix. P-values are then obtained using permutations. Some examples of the method are given for tests involving several factors, including factorial and hierarchical (nested) designs and tests of interactions.},
-author = {Anderson, Marti J.},
-doi = {10.1111/j.1442-9993.2001.01070.pp.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anderson - 2001 - A new method for non‐parametric multivariate analysis of variance.pdf:pdf},
-journal = {Austral ecology},
-pages = {32--46},
-title = {{A new method for non-parametric multivariate analysis of variance}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1442-9993.2001.01070.pp.x/full},
-volume = {26},
-year = {2001}
-}
-@article{Mouillot1999,
-abstract = {Although having been much criticized, diversity indices are still widely used in animal and plant ecology to evaluate, survey, and conserve ecosystems. It is possible to quantify biodiversity by using estimators for which statistical characteristics and performance are, as yet, poorly defined. In the present study, four of the most frequently used diversity indices were compared: the Shannon index, the Simpson index, the Camargo eveness index, and the Pielou regularity index. Comparisons were performed by simulating the Zipf-Mandelbrot parametric model and estimating three statistics of these indices, i.e., the relative bias, the coefficient of variation, and the relative root-mean-squared error. Analysis of variance was used to determine which of the factors contributed most to the observed variation in the four diversity estimators: abundance distribution model or sample size. The results have revealed that the Camargo eveness index tends to demonstrate a high bias and a large relative root-mean-squared error whereas the Simpson index is least biased and the Shannon index shows a smaller relative root-mean-squared error, regardless of the abundance distribution model used and even when sample size is small. Shannon and Pielou estimators are sensitive to changes in species abundance pattern and present a nonnegligible bias for small sample sizes ({\textless}1000 individuals).},
-annote = {Cited By (since 1996): 37
-Export Date: 28 December 2011
-Source: Scopus
-CODEN: KOGSB
-Language of Original Document: English
-Correspondence Address: Mouillot, D.; Lab. d'Ecologie Mediterraneenne, Universit{\~{A}}{\textcopyright} de Corse, BP 52, 20250 Corte, France; email: mouillot@oec.fr},
-author = {Mouillot, David and Lepr{\^{e}}tre, Alain},
-doi = {10.1007/s101440050024},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouillot, Lepr{\^{e}}tre - 1999 - A comparison of species diversity estimators.pdf:pdf},
-journal = {Researches on Population Ecology},
-number = {2},
-pages = {203--215},
-title = {{A comparison of species diversity estimators}},
-url = {http://link.springer.com/article/10.1007{\%}2Fs101440050024},
-volume = {41},
-year = {1999}
-}
-@article{Struyk1972,
-author = {Struyk, Raymond J.},
-doi = {10.2307/142874},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Struyk - 1972 - Spatial concentration of manufacturing employment in metropolitan areas some empirical evidence.pdf:pdf},
-journal = {Economic Geography},
-number = {2},
-pages = {189--1992},
-title = {{Spatial concentration of manufacturing employment in metropolitan areas: some empirical evidence}},
-url = {http://www.jstor.org/stable/142874},
-volume = {48},
-year = {1972}
-}
-@article{Gregorius2008,
-abstract = {Simpson's index of diversity equals the probability of drawing without replacement two individuals of different type from a given collection. The interpretation of its inverse as the effective number of types reflects the biological meaning of diversity as the multiformity of the collection. The effective number of types is maximal, equalling the total number of types, only if all types are uniformly distributed. Simpson's diversity thus fulfills one of the most basic conceptual criteria for diversity measures. The criterion does not, however, directly carry over to continuously varying differences between types. It is shown that the common practice of taking averages or special sums of differences cannot serve as the desired generalization. In a new approach, the probabilistic interpretation of Simpson's index is used to extend the basic criterion of diversity to arbitrary differences between types, thereby retaining the concept of effective number. By considering ? as the resolution at which differences between individuals distinguish them, we define diversity as the probability D(?) of sampling without replacement two individuals that differ by more than ?. It is pointed out that this measure generalizes the classical Simpson-criterion of diversity in that it applies to any decomposition of the collection into groups, such that individuals within a group differ by at most ? and between groups by at least ?. Maximum diversity is reached if all groups are of equal size. This maximum property of the new measure motivates definition of the effective number of types at resolution ? independently of any particular decomposition into groups and while maintaining the basic diversity criterion. The advantages of and newinsights to be derived fromthis scale-free measure are demonstrated by suggesting an approach to ?-diversity in ecology that is consistent with the criterion of diversity and by providing a worked example in population genetics using multiple-loci microsatellite data from three wild cherry populations. The example shows that gene associations may strongly affect the ranking of populations for genetic diversity},
-author = {Gregorius, Hans-Rolf and Gillet, Elizabeth M.},
-doi = {10.1016/j.ecolmodel.2007.08.026},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gregorius, Gillet - 2008 - Generalized Simpson-diversity.pdf:pdf},
-journal = {Ecological Modelling},
-number = {1-2},
-pages = {90--96},
-title = {{Generalized Simpson-diversity}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0304380007004255},
-volume = {211},
-year = {2008}
-}
-@article{Umana2015,
-abstract = {One of the few rules in ecology is that communities are composed of many rare and few common species. Trait-based investigations of abundance distributions have generally focused on species-mean trait values with mixed success. Here, using large tropical tree seedling datasets in China and Puerto Rico, we take an alternative approach that considers the magnitude of intraspecific variation in traits and growth as it relates to species abundance. We find that common species are less variable in their traits and growth. Common species also occupy core positions within community trait space indicating that they are finely tuned for the available conditions. Rare species are functionally peripheral and are likely transients struggling for success in the given environment. The work highlights the importance of considering intraspecific variation in trait-based ecology and demonstrates asymmetry in the magnitude of intraspecific variation among species is critical for understanding of how traits are related to abundance.},
-author = {Uma{\~{n}}a, Mar{\'{i}}a Natalia and Zhang, Caicai and Cao, Min and Lin, Luxiang and Swenson, Nathan G.},
-doi = {10.1111/ele.12527},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Uma{\~{n}}a et al. - 2015 - Commonness, rarity, and intraspecific variation in traits and performance in tropical tree seedlings.pdf:pdf},
-journal = {Ecology Letters},
-number = {12},
-pages = {1329--1337},
-title = {{Commonness, rarity, and intraspecific variation in traits and performance in tropical tree seedlings}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12527/abstract},
-volume = {18},
-year = {2015}
-}
-@article{Kieu1996,
-abstract = {We consider a random measure for which distribution is invariant under the action of a standard transformation group. The reduced moments are defined by applying classical theorems on invariant measure decomposition. We present a general method for constructing unbiased estimators of reduced moments. Several asymptotic results are established under an extension of the Brillinger mixing condition. Examples related to stochastic geometry are given.},
-annote = {R{\'{e}}sum{\'{e}} seulement. L'article complet n'est pas publi{\'{e}}.},
-author = {Ki{\^{e}}u, Kien and Mora, Marianne},
-doi = {10.1017/S0001867800008946},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ki{\^{e}}u, Mora - 1999 - Estimating the reduced moments of a random measure.pdf:pdf},
-journal = {Advances in Applied Probability},
-number = {1},
-pages = {48--62},
-title = {{Estimating the reduced moments of a random measure}},
-url = {https://doi.org/10.1017/S0001867800008946},
-volume = {31},
-year = {1999}
-}
-@article{Benedetti-Cecchi2003,
-abstract = {Experiments in ecology are usually designed to provide tests of hypotheses on the influence of the mean intensity of causal processes, whereas the variance around mean effects has been largely overlooked as a causal force in biological assemblages. Repetition of experiments in space and time provides an estimate of this variability at specific scales, but does not explain how changes in variance generate structure in assemblages and the extent to which variance and mean intensity interact. This paper seeks to identify suitable procedures for empirical analyses on the influence of variance and mean intensity of predictor ecological variables on spatial and temporal patterns in natural populations. A survey of the ecological literature indicates that temporal variability in studies of disturbance and in analyses of consumer-resource interactions is generally expressed in terms of frequency of events. This is inappropriate, as frequency confounds the variance with the mean effect size of a process. A possible solution to the problem involves experimental designs in which levels of intensity and those of variability are chosen independently over explicit spatial or temporal scales and treated as fixed, orthogonal factors. Examples are offered for various scenarios of consumer-resource interactions along with indications for statistical tests of hypotheses. Such novel approaches have important ramifications for understanding variability in a wide range of ecological contexts and for predicting the response of assemblages to increased environmental fluctuations, including those expected under modified climate conditions.},
-author = {Benedetti-Cecchi, Lisandro},
-doi = {10.1890/02-8011},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Benedetti-Cecchi - 2003 - The importance of the variance around the mean effect size of ecological processes.pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2335--2346},
-title = {{The importance of the variance around the mean effect size of ecological processes}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/02-8011/abstract},
-volume = {84},
-year = {2003}
-}
-@article{Bonneu2009,
-abstract = {The problem of finding an optimal location frequently occurs in geomarketing, economics and other fields: positioning a new branch of a bank, a supermarket, a fire station, a plant, designing a traffic network, etc. The optimal location of the source facility is the argument-minimum of an optimization problem parametrized by some characteristics of the clients. The random nature of some of these characteristics has already been recognized, but few stochastic models for location-allocation problems address the issue of uncertainty of the locations of the clients, and even then they do it with very naive tools. It is proposed to recognize uncertainty in the spatial positions of the clients, and possible spatial autocorrelation as well, by considering the random inputs of the optimization as one realization of a spatial marked point process. The method, called SPP location-allocation, involves fitting a point process model, simulating from the adjusted process, and solving a family of optimization problems for each simulated set of observations. The advantage of this approach over the deterministic one is twofold: it gives an indication of the spatial variability of the optimal solution, and it allows one to solve larger problems. Finally an application to the optimal positioning of a new fire station in the Toulouse area (France) is presented with some heuristic algorithms. (c) 2008 Elsevier B.V. All rights reserved.},
-annote = {ISI Document Delivery No.: 438QR
-Times Cited: 2
-Cited Reference Count: 30
-Bonneu, Florent Thomas-Agnan, Christine
-ELSEVIER SCIENCE BV
-Sp. Iss. SI},
-author = {Bonneu, Florent and Thomas-Agnan, Christine},
-doi = {10.1016/j.csda.2008.10.016},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonneu, Thomas-Agnan - 2009 - Spatial point process models for location-allocation problems.pdf:pdf},
-journal = {Computational Statistics {\&} Data Analysis},
-number = {8},
-pages = {3070--3081},
-title = {{Spatial point process models for location-allocation problems}},
-volume = {53},
-year = {2009}
-}
-@article{Sheather1991,
-abstract = {We present a new method for data-based selection of the bandwidth in kernel density estimation which has excellent properties. It improves on a recent procedure of Park and Marron (which itself is a good method) in various ways. First, the new method has superior theoretical performance; second, it also has a computational advantage; third, the new method has reliably good performance for smooth densities in simulations, performance that is second to none in the existing literature. These methods are based on choosing the bandwidth to (approximately) minimize good quality estimates of the mean integrated squared error. The key to the success of the current procedure is the reintroduction of a non-stochastic term which was previously omitted together with use of the bandwidth to reduce bias in estimation without inflating variance.},
-author = {Sheather, S. J. and Jones, M. C.},
-doi = {10.2307/2345597},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sheather, Jones - 1991 - A Reliable Data-Based Bandwidth Selection Method for Kernel Density Estimation.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {3},
-pages = {683--690},
-title = {{A Reliable Data-Based Bandwidth Selection Method for Kernel Density Estimation}},
-url = {http://dx.doi.org/10.2307/2345597},
-volume = {53},
-year = {1991}
-}
-@article{Ares2003,
-abstract = {Arid and semiarid shrublands occupy extensive land areas over the world, are susceptible to desertification by anthropic use and can contribute to regional climate change. These prompt the interest to monitor and evaluate these lands adequately in order to detect early stages of degradation. Evaluation topics must refer to biology-relevant characteristics of these systems, while simultaneously satisfying sampling consistency over extended landscape areas. We present an analysis of process-relevant parameters related to changes in the spatial arrangement of the plant canopy of shrublands inferred from high-resolution panchromatic aerial photos and Interferometric Synthetic Aperture Radar imagery. We obtained low-altitude images systematically located along several gradients of land-use intensity in a Patagonian Monte shrubland in Argentina. Images were digitized to spatial resolutions ranging from 0.09 to 0.72 m (pixel size) and the average values and an-isotropic characteristics of the plant canopy patterns were quantified by means of a Fourier metric. We used radar-derived imagery to overlay the panchromatic images on a digital elevation model in order to study the correspondence of potential runoff patterns and the spatial arrangement of plants. We related an-isotropic features of the plant canopy images to the prevailing wind regime. Observed trends were further interpreted on the basis of a spatial-explicit simulation model describing the dynamics of the main functional groups in the plant community. We conclude that early stages of anthropic-driven dryland degradation in the Patagonian Monte can be characterized by the incipient un-coupling of spatial vegetation patterns from those of runoff at a landscape scale, and a progressive coupling to the spatial pattern of the wind regime. The method and metrics we present can be used to quantify early desertification changes in other similar drylands at extended spatial scales.},
-annote = {Article},
-author = {Ares, Jorge and {Del Valle}, H{\'{e}}ctor and Bisigato, Alejandro},
-doi = {10.1046/j.1365-2486.2003.00690.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ares, Del Valle, Bisigato - 2003 - Detection of process-related changes in plant patterns at extended spatial scales during early drylan.pdf:pdf},
-journal = {Global Change Biology},
-number = {11},
-pages = {1643--1659},
-title = {{Detection of process-related changes in plant patterns at extended spatial scales during early dryland desertification}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2486.2003.00690.x/full},
-volume = {9},
-year = {2003}
-}
-@article{Rosatti2015,
-abstract = {Originality measures how different a given species is from all other co-occurring species regarding either their phylogenetic history or functional traits. Since it is important to preserve the various aspects of diversity and original species carry more phylogenetic or functional information, originality may be used to assign conservation priorities. Our goal was to evaluate the relationships between phylogenetic and functional originalities, and their simulated losses under extinction scenarios based on abundance, fire tolerance and habitat preference. We placed 100 plots in a cerrado reserve located in central Brazil, sampled all woody plants species within the plots, measured 14 functional traits and measured fire history. We assembled a phylogenetic tree and a functional dendrogram, with which we calculated the originalities. Phylogenetic- and functional-based originalities were correlated. However, the loss of functional originality was different from random extinctions on the abundance and fire tolerance scenarios, whereas the loss of phylogenetic originality was not. When compared with phylogenetic originality, functional originality brought more information to be used in conservation strategies because it was sensitive to differences in species abundance and fire tolerance. Thus, the extinction of rare or fire-sensitive species would result in important functional changes due to loss of distinctive traits.},
-author = {Rosatti, Natalia Bianca and Silva, Danilo Muniz and Batalha, Marco Ant{\^{o}}nio},
-doi = {10.1111/aec.12210},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rosatti, Silva, Batalha - 2015 - Loss of phylogenetic and functional originalities of woody cerrado species in simulated extinction scen.pdf:pdf},
-journal = {Austral Ecology},
-number = {3},
-pages = {267--274},
-title = {{Loss of phylogenetic and functional originalities of woody cerrado species in simulated extinction scenarios}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/aec.12210/abstract},
-volume = {40},
-year = {2015}
-}
-@article{Motomura1932,
-author = {Motomura, I.},
-journal = {Zoological Magazine},
-language = {Japanese},
-pages = {379--383},
-title = {{On the statistical treatment of communities}},
-volume = {44},
-year = {1932}
-}
-@article{Kingham1995,
-abstract = {An approach to analysing data for spatial clustering is outlined, with special reference to environmental epidemiology. The method is based on recent developments in spatial point-process modelling; specifically, on the use of so-called ‘second-order' analysis of bivariate point patterns. This continuous-space approach offers some advantages over analytical methods that aggregate health events to areal units. The method is implemented within the framework of a proprietary geographical information system, ARC/INFO, and is illustrated with reference to health data from a questionnaire survey of children in Preston (Lancashire). The nature of the data gained from the questionnaire means that variables which may affect the health of the children studied can be accounted for within the analysis.},
-author = {Kingham, S. P. and Gatrell, Antony C. and Rowlingson, Barry S.},
-doi = {10.1068/a270809},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kingham, Gatrell, Rowlingson - 1995 - Testing for Clustering of Health Events within a Geographical Information System Framework.pdf:pdf},
-journal = {Environment and Planning A},
-number = {5},
-pages = {809--821},
-title = {{Testing for Clustering of Health Events within a Geographical Information System Framework}},
-url = {http://journals.sagepub.com/doi/abs/10.1068/a270809},
-volume = {27},
-year = {1995}
-}
-@article{Anas1998,
-abstract = {An interview with Chicago's current mayor, Richard M. Daley: 'New York is too big this way,' the mayor says, raising a thick hand over his head. Stretching both arms out at his sides, he adds, 'Los Angeles is too big this way. All the other cities are too small. We're just right.' (Bailey and Coleman, 1996, p. 6) Mayor Daley is catering to a widespread fascination with the roles that urban size and structure play in people's lives. Academic as well as other observers have long sought explanations for urban development patterns and criteria by which to judge their desirability. Furthermore, as we shall see, understanding the organization of cities yields insights about economy-wide growth processes and sheds light on economic concepts of long standing interest: returns to scale, monopolistic competition, vertical integration, technological innovation, innovation diffusion, and international specialization. Cities also are prime illustrations of some newer academic interests such as complex structural evolution and self-organization.},
-author = {Anas, Alex and Arnott, Richard and Small, Kenneth A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Anas, Arnott, Small - 1998 - Urban Spatial Structure.pdf:pdf},
-journal = {Journal of Economic Literature},
-number = {3},
-pages = {1426--1464},
-title = {{Urban Spatial Structure}},
-url = {http://www.jstor.org/stable/2564805},
-volume = {36},
-year = {1998}
-}
-@techreport{Decrop2002,
-abstract = {L'objectif de ce working paper est d'effectuer une analyse descriptive de l'agglom{\'{e}}ration g{\'{e}}ographique des activit{\'{e}}s {\'{e}}conomiques et de son {\'{e}}volution r{\'{e}}cente (p{\'{e}}riode 1994-2000).},
-address = {Bruxelles},
-author = {Decrop, J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Decrop - 2002 - Agglom{\'{e}}ration et dynamiques des activit{\'{e}}s {\'{e}}conomiques des villes belges, une approche spatiale et sectorielle.pdf:pdf},
-pages = {106},
-publisher = {Bureau F{\'{e}}d{\'{e}}ral du Plan},
-title = {{Agglom{\'{e}}ration et dynamiques des activit{\'{e}}s {\'{e}}conomiques des villes belges, une approche spatiale et sectorielle}},
-url = {http://www.plan.be/publications/publication-170-fr-agglomeration+et+dynamique+des+activites+economiques+dans+les+villes+belges+une+approche+spatiale+et+sectorielle},
-year = {2002}
-}
-@techreport{Matheron1970,
-address = {Fontainebleau, France},
-author = {Matheron, Georges},
-booktitle = {Les cahiers du Centre de Morphologie Math{\'{e}}matique de Fontainebleau},
-pages = {9--57},
-title = {{La th{\'{e}}orie des variables regionalis{\'{e}}es et ses applications}},
-year = {1970}
-}
-@article{Ricotta2014b,
-abstract = {Aims Measures of plot-to-plot phylogenetic dissimilarity and beta diversity are providing a powerful tool for understanding the complex ecological and evolutionary mechanisms that drive community assembly. Methods Here, we review the properties of some previously published dissimilarity measures that are based on minimum or average phylogenetic dissimilarity between species in different plots. Important Findings We first show that some of these measures violate the basic condition that for two identical plots the measures take the value zero. They also violate the condition that the dissimilarity between two identical plots should always be lower than that between two different plots. Such erratic behavior renders these measures unsuitable for measuring plot-to-plot phylogenetic dissimilarity. We next propose a new measure that satisfies these conditions, thus providing a more reasonable way for measuring phylogenetic dissimilarity.},
-author = {Ricotta, Carlo and Bacaro, Giovanni and Pavoine, Sandrine},
-doi = {10.1093/jpe/rtu008},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Bacaro, Pavoine - 2014 - A cautionary note on some phylogenetic dissimilarity measures.pdf:pdf},
-journal = {Journal of Plant Ecology},
-number = {1},
-pages = {12--16},
-title = {{A cautionary note on some phylogenetic dissimilarity measures}},
-url = {http://jpe.oxfordjournals.org/cgi/doi/10.1093/jpe/rtu008},
-volume = {8},
-year = {2014}
-}
-@article{Wiegand2006,
-abstract = {1 We use a grid- and simulation-based approach to extend point pattern analysis to deal with plants of finite size and irregular shape, and compare the results of our approach with that of the conventional point approximation. The plants are approximated by using an underlying grid and may occupy several adjacent grid cells depending on their size and shape. Null models correspond to that of point pattern analysis but need to be modified to account for the finite size and irregular shape of plants. 2 We use a mapped area of a grass-shrub steppe in semi-arid Patagonia, Argentina, to show that the shrub community is essentially randomly structured, but that shrubs facilitate grasses in their immediate neighbourhood. 3 The occurrence of this random spatial structure provides important new information on the biology of shrub populations. In general, previous data from semi-arid and arid ecosystems have shown that adult shrubs tend to show over-dispersed patterns, whereas juveniles are clumped. 4 We find that the point approximation may produce misleading results (i) if plant size varies greatly, (ii) if the scale of interest is of the same order of magnitude as the size of the plants, and (iii) if the plants of a given pattern are constrained through competition for space by the presence of other plants. The point approximation worked well in all other cases, but usually depicted weaker significant effects than when the size and shape of plants were taken into account. 5 Our approach to quantifying small-scale spatial patterns in plant communities has broad applications, including the study of facilitation and competition. Ecologists will be able to use the software available to take advantage of these methods.},
-annote = {ISI Document Delivery No.: 048UT},
-author = {Wiegand, Thorsten and Kissling, W. Daniel and Cipriotti, Pablo A. and Aguiar, Mart{\'{i}}n R.},
-doi = {10.1111/j.1365-2745.2006.01113.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand et al. - 2006 - Extending point pattern analysis for objects of finite size and irregular shape(2).pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {825--837},
-title = {{Extending point pattern analysis for objects of finite size and irregular shape}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2006.01113.x/full},
-volume = {94},
-year = {2006}
-}
-@misc{Cirad2008,
-author = {Cirad},
-title = {{La Charte informatique du Cirad}},
-url = {http://intranet-dsi.cirad.fr/content/download/1699/9702/file/charte informatique Cir2008.pdf},
-year = {2008}
-}
-@article{Lucas1988,
-abstract = {This paper considers the prospects for constructing a neoclassical theory of growth and international trade that is consistent with some of the main features of economic development. Three models are considered and compared to evidence: a model emphasizing physical capital accumulation and technological change, a model emphasizing human capital accumulation through schooling, and a model emphasizing specialized human capital accumulation through learning-by-doing.},
-author = {Lucas, Robert E.},
-doi = {10.1016/0304-3932(88)90168-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lucas - 1988 - On the mechanics of economic development.pdf:pdf},
-journal = {Journal of Monetary Economics},
-number = {1},
-pages = {3--42},
-title = {{On the mechanics of economic development}},
-url = {http://www.sciencedirect.com/science/article/pii/0304393288901687},
-volume = {22},
-year = {1988}
-}
-@article{Zimmerman1993,
-abstract = {A test for the randomness of a mapped spatial pattern of events in a rectangle D in R² is examined that is based on the 'distance' between the bivariate empirical distribution function of the events' Cartesian co-ordinates and the uniform distribution function. The distance between distribution functions is measured by a modification of the bivariate Cramer-von Mises statistic that is invariant to the corner of D identified as the origin. This invariance property, which is essential, is lacking in the standard bivariate Cramer-von Mises statistic. Several real examples and results from simulation indicate that the test proposed is superior to existing tests for detecting heterogeneous alternatives to spatial randomness but inferior for detecting regular or aggregated alternatives. Some additional features of the test are its computational simplicity, the non-necessity of adjusting for edge effects and the ease with which it can be extended to test for certain types of heterogeneity.},
-author = {Zimmerman, Dale L.},
-doi = {10.2307/2347408},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zimmerman - 1993 - A Bivariate Cramer-von Mises Type of Test for Spatial Randomness.pdf:pdf},
-journal = {Applied Statistics},
-number = {1},
-pages = {43--54},
-title = {{A Bivariate Cramer-von Mises Type of Test for Spatial Randomness}},
-url = {https://www.jstor.org/stable/2347408},
-volume = {42},
-year = {1993}
-}
-@unpublished{Arbia2015,
-abstract = {The presence of knowledge spillovers and shared human capital is at the heart of the Marhall-Arrow- Romer externalities hypothesis. Most of the earlier empirical contributions on knowledge externalities, however, considered data aggregated at a regional level so that conclusions are based on the arbitrary definition of jurisdictional spatial units: this is the essence of the so-called Modifiable Areal Unit Problem. A second limitation of these studies is constituted by the fact that, somewhat surprisingly, while concentrating on the effects of agglomeration on firm creation and growth, the literature has, conversely, largely ignored its effects on firm survival. The present paper aims at contributing to the existing literature by answering to some of the open methodological questions reconciling the literature of Cox proportional hazard with that on point pattern and thus capturing the true nature of spatial information. We also present some empirical results based on Italian firm demography data collected and managed by the Italian National Institute of Statistics (ISTAT). Keywords:},
-author = {Arbia, Giuseppe and Espa, Giuseppe and Filipponi, Danila and Giuliani, Diego},
-booktitle = {DEM Discussion Papers},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia et al. - 2015 - A spatial and sectoral analysis of firm demography in Italy.pdf:pdf},
-institution = {Univerist{\`{a}} degli studi di Trento},
-pages = {1--17},
-title = {{A spatial and sectoral analysis of firm demography in Italy}},
-year = {2015}
-}
-@article{Schnitzer2001,
-abstract = {The maintenance of species diversity by treefall gaps is a long-standing paradigm in forest ecology. Gaps are presumed to provide an environment in which tree species of differing competitive abilities partition heterogeneous resources. The empirical evidence to support this paradigm, however, remains scarce, and some recent studies even suggest that gaps do not maintain the diversity of shade-tolerant species. Although there is evidence that gaps maintain the diversity of pioneer trees, most of this evidence comes from studies that did not make comparisons between gaps and intact forest sites (controls). Further, nearly all studies on the maintenance of diversity by gaps have ignored lianas, an important component of both old-world and neotropical forests. We tested the hypothesis that treefall gaps maintain shade-tolerant tree, pioneer tree, and liana species diversity in an old-growth forest on Barro Colorado Island (BCI), Panama. We compared the density and species richness of these guilds between paired gap and non-gap sites on both a per- area and a per-individual (per capita) basis. We found no difference in shade-tolerant tree density and species richness between the gap and non-gap sites. Both pioneer tree and liana density and species richness, however, were significantly higher in the gap than in the non- gap sites on both a per-area and a per-individual basis. These results suggest that gaps maintain liana species diversity and that this effect is not merely a consequence of increased density. Furthermore, our data confirm the long-held belief that gaps maintain pioneer tree species diversity. Because lianas and pioneer trees combined account for ?43{\%} of the woody plant species on BCI, and in other forests, our results are likely to be broadly applicable and suggest that gaps play a strong role in the maintenance of woody species diversity.},
-author = {Schnitzer, Stefan A. and Carson, Walter P.},
-doi = {10.1890/0012-9658(2001)082[0913:TGATMO]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schnitzer, Carson - 2001 - Treefall Gaps and the Maintenance of Species Diversity in a Tropical Forest.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {913--919},
-title = {{Treefall Gaps and the Maintenance of Species Diversity in a Tropical Forest}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658{\%}282001{\%}29082[0913:TGATMO]2.0.CO{\%}3B2/abstract},
-volume = {82},
-year = {2001}
-}
-@book{Richards2010,
-abstract = {There is long-standing disagreement among systematists about how to divide biodiversity into species. Over twenty different species concepts are used to group organisms, according to criteria as diverse as morphological or molecular similarity, interbreeding and genealogical relationships. This, combined with the implications of evolutionary biology, raises the worry that either there is no single kind of species, or that species are not real. This book surveys the history of thinking about species from Aristotle to modern systematics in order to understand the origin of the problem, and advocates a solution based on the idea of the division of conceptual labor, whereby species concepts function in different ways – theoretically and operationally. It also considers related topics such as individuality and the metaphysics of evolution, and how scientific terms get their meaning. This important addition to the current debate will be essential for philosophers and historians of science, and for biologists.},
-address = {Cambridge},
-author = {Richards, Richard A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Richards - 2010 - The Species Problem. A Philosophical Analysis.pdf:pdf},
-isbn = {9780521196833},
-publisher = {Cambridge University Press},
-title = {{The Species Problem. A Philosophical Analysis}},
-year = {2010}
-}
-@article{Chao2014,
-abstract = {Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number qD, where q = 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q {\textgreater} 0) and present a unified approach for both individual-based (abundance) data and samplebased (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q = 0 (species richness), q = 1 (the exponential of Shannon's entropy index), and q = 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants. {\textcopyright} 2014 by the Ecological Society of America.},
-annote = {Export Date: 25 February 2014
-Source: Scopus},
-author = {Chao, Anne and Gotelli, Nicholas J. and Hsieh, T. C. and Sander, Elizabeth L. and Ma, K. H. and Colwell, Robert K. and Ellison, Aaron M.},
-doi = {10.1890/13-0133.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao et al. - 2014 - Rarefaction and extrapolation with Hill numbers A framework for sampling and estimation in species diversity studie.pdf:pdf},
-journal = {Ecological Monographs},
-number = {1},
-pages = {45--67},
-title = {{Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies}},
-url = {http://www.esajournals.org/doi/abs/10.1890/13-0133.1},
-volume = {84},
-year = {2014}
-}
-@book{Weber1929,
-address = {Chicago},
-author = {Weber, Alfred},
-publisher = {The University of Chicago Press},
-title = {{Theory of the Location of Industries}},
-year = {1929}
-}
-@article{Mouillot2005,
-abstract = {The concept of niche overlap appears in studies of the mechanisms of the maintenance of species diversity, in searches for assembly rules, and in estimation of within-community species redundancy. For plant traits measured on a continuous scale, existing indices are inadequate because they split the scale into a number of categories thus losing information. An index is easy to construct if we assume a normal distribution for each trait within a species, but this assumption is rarely true. We extend and apply an index, NOK, which is based on kernel density functions, and can therefore work with distributions of any shape without prior assumptions. For cases where the ecologist wishes to downweight traits that are inter-correlated, we offer a variant that does this: NOKw. From either of these indices, an index of the mean niche overlap in a community can be calculated: NOK,community and NOKw,community. For all these indices, the variance can be calculated and formulae for this are given. To give examples of the new indices in use, we apply them to a coastal fish dataset and a sand-dune plant dataset. The former exhibits considerable non-normality, emphasising the need for kernel-based indices. Accordingly, there was a considerable difference in index values, with those for an index based on a normal distribution being significantly higher than those from an index which, being based on kernel fitting, is not biased by an assumption for the distribution. The NOK values were ecologically consistent for the fish species concerned, varying from 0.02 to 0.53. The sand-dune plant data also showed a wide range of overlap values. Interestingly, the least overlap was between two graminoids, which would have been placed in the same functional group in the coarse classification often used in functional-type/ecosystem-function work.},
-author = {Mouillot, David and Stubbs, Wendy and Faure, Matthieu and Dumay, Olivier and Tomasini, Jean-Antoine and Wilson, J. Bastow and Chi, Thang Do},
-doi = {10.1007/s00442-005-0151-z},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouillot et al. - 2005 - Niche overlap estimates based on quantitative functional traits a new family of non-parametric indices.pdf:pdf},
-journal = {Oecologia},
-number = {3},
-pages = {345--353},
-title = {{Niche overlap estimates based on quantitative functional traits: a new family of non-parametric indices}},
-volume = {145},
-year = {2005}
-}
-@article{Villeger2013,
-abstract = {Aim One of the main gaps in the assessment of biodiversity is the lack of a unified framework for measuring its taxonomic and functional facets and for unveiling the underlying patterns. Location Europe, 25 large river basins. Methods Here, we develop a decomposition of functional b-diversity, i.e. the dissimilarity in functional composition between communities, into a functional turnover and a functional nestedness-resultant component. Results We found that functional b-diversity was lower than taxonomic b-diversity. This difference was driven by a lower functional turnover compared with taxonomic turnover while the nestedness-resultant component was similar for taxonomic and functional b-diversity. Main conclusions Fish faunas with different species tend to share the same functional attributes. The framework presented in this paper will help to analyse biogeographical patterns as well as to measure the impact of human activities on the functional facets of biodiversity.},
-author = {Vill{\'{e}}ger, S{\'{e}}bastien and Grenouillet, Ga{\"{e}}l and Brosse, S{\'{e}}bastien},
-doi = {10.1111/geb.12021},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vill{\'{e}}ger, Grenouillet, Brosse - 2013 - Decomposing functional $\beta$-diversity reveals that low functional $\beta$-diversity is driven by low funct.pdf:pdf},
-journal = {Global Ecology and Biogeography},
-number = {6},
-pages = {671--681},
-title = {{Decomposing functional $\beta$-diversity reveals that low functional $\beta$-diversity is driven by low functional turnover in European fish assemblages}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12021/abstract},
-volume = {22},
-year = {2013}
-}
-@article{Autant-Bernard1999,
-author = {Autant-Bernard, Corinne and Massard, Nadine},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Autant-Bernard - 1999 - G{\'{e}}ographie des externalit{\'{e}}s de connaissance et proximit{\'{e}} technologiques.pdf:pdf},
-journal = {Economie Appliqu{\'{e}}e},
-number = {4},
-pages = {35--68},
-title = {{Econom{\'{e}}trie des externalit{\'{e}}s technologiques locales et g{\'{e}}ographie de l'innovation : une analyse critique}},
-volume = {52},
-year = {1999}
-}
-@article{Connell1978,
-abstract = {The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.},
-author = {Connell, Joseph H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Connell - 1978 - Diversity in Tropical Rain Forests and Coral Reefs.pdf:pdf},
-journal = {Science},
-number = {4335},
-pages = {1302--1310},
-title = {{Diversity in Tropical Rain Forests and Coral Reefs}},
-volume = {199},
-year = {1978}
-}
-@article{Paine2011,
-abstract = {Niche diff erentiation and ecological fi ltering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche diff erentiation and environmental fi ltering, then tested these predictions with a dataset of 4672 trees located in nine 1-ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specifi c leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. Th ere was far more evidence for environmental fi ltering than for niche diff erentiation in these forests. Furthermore, we contrasted results from species-mean and individual-level trait values. Analyses that took within-species trait variation into account were far more sensitive indicators of niche diff erentiation and ecological fi ltering. Speciesmean analyses, by contrast, may underestimate the eff ects of ecological processes on community assembly. Environmental fi ltering appeared somewhat more intense on leaf traits than on stem traits, whereas niche diff erentiation aff ected neither strongly. By accounting for within-species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche diff erentiation and environmental fi ltering may be more pervasive than previously believed.},
-author = {Paine, C. E. Timothy and Baraloto, Christopher and Chave, J{\'{e}}r{\^{o}}me and H{\'{e}}rault, Bruno},
-doi = {10.1111/j.1600-0706.2010.19110.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Paine et al. - 2011 - Functional traits of individual trees reveal ecological constraints on community assembly in tropical rain forests.pdf:pdf},
-journal = {Oikos},
-number = {5},
-pages = {720--727},
-title = {{Functional traits of individual trees reveal ecological constraints on community assembly in tropical rain forests}},
-url = {http://doi.wiley.com/10.1111/j.1600-0706.2010.19110.x},
-volume = {120},
-year = {2011}
-}
-@techreport{Behrens2013,
-abstract = {We document the location patterns of Canadian manufacturing industries – as well as changes in those patterns over the first decade of 2000 – using detailed micro-geographic data. Depending on industry definitions and years, 40 to 60 percent of industries are clustered. According to our measures, manufacturing industries become less geographically concentrated in Canada, i.e., localization is decreasing. Yet, some of the most localized industries are becoming even more localized. We also document the locational trends specific to small firms, young firms, and exporters. We find that their location patterns do not differ significantly from that of the other firms in their industries.},
-author = {Behrens, Kristian and Bougna, Th{\'{e}}ophile},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Behrens, Bougna - 2013 - An Anatomy of the Geographical Concentration of Canadian Manufacturing Industries.pdf:pdf},
-publisher = {CIRP{\'{E}}E},
-title = {{An Anatomy of the Geographical Concentration of Canadian Manufacturing Industries}},
-year = {2013}
-}
-@article{Chao1988,
-abstract = {A generalized form of Good's estimator (Good, 1953) is proposed to estimate the coverage of a random sample from an unknown multinomial distribution. Some properties of the proposed estimator are derived. This generalized estimator retains all good properties of Good's estimator and has smaller bias if each cell probability is less than 0.5. The results of a simulation study are reported to compare the performance of the proposed method with that of other existing estimators.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Chao, Anne and Lee, Shen-Ming and Chen, T.-C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Lee, Chen - 1988 - A generalized Good's nonparametric coverage estimator.pdf:pdf},
-journal = {Chinese Journal of Mathematics},
-pages = {189--199},
-title = {{A generalized Good's nonparametric coverage estimator}},
-url = {http://www.jstor.org/stable/43836340},
-volume = {16},
-year = {1988}
-}
-@article{Picard2009,
-abstract = {1. Considering that the spatial pattern of trees is a footprint of the biological processes that drive their dynamics, increasing work has been undertaken to analyse spatial patterns and fit spatial point processes to them. When diameter is taken into account, the underlying point process is a marked point process. The question then is how to correctly model the dependence between the mark and location, and the different patterns at the different scales, to gain understanding of the underlying biological processes. 2. The data used comes from the Paracou rain forest in French Guiana (5 ° 15 ′ N, 52 ° 55 ′ W). The spatial pattern of trees in this forest exhibits regularity at small distances ( c. 6 m) and clustering at larger distances ( c. 30 m). The pattern is linked to diameter, with a shift from clustering to regularity as trees grow. 3. Two models of spatial pattern are used. The first one is pattern-driven in the sense that it breaks down the observed pattern into a mixture of regular, clustered and random contributions. The second one is process-based and uses a simple individual-based space-dependent model of forest dynamics as a simulation algorithm. It is obtained as the limit of this spatio-temporal model when time tends to infinity. 4. Both models are consistent with the observed pattern, with a better fit provided by the second model. Moreover this second model provides a biological interpretation of the observed pattern in terms of forest dynamics. However the first model's implementation is simpler (both for simulation and for parameter estimation). 5. Synthesis. Modelling the spatial pattern of plants using spatial point processes gives insights into the biological processes that drive their dynamics. It allows the reconstruction of their dynamics given only a snapshot of plant locations. Very few solutions exist to model complex marked spatial patterns when point location and mark are dependent. We defined and compared two point processes that successfully modelled the spatial pattern of trees in a rain forest with interaction between tree location and tree size. Both models highlight competition (either symmetric or asymmetric) as a driving process towards regularity. The second model further reveals a self- organizing dynamic with a feedback effect of competition.},
-author = {Picard, Nicolas and Bar-Hen, Avner and Mortier, Fr{\'{e}}d{\'{e}}ric and Chadoeuf, Jo{\"{e}}l},
-doi = {10.1111/j.1365-2745.2008.01445.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Picard et al. - 2009 - Understanding the dynamics of an undisturbed tropical rain forest from the spatial pattern of trees(2).pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {97--108},
-title = {{Understanding the dynamics of an undisturbed tropical rain forest from the spatial pattern of trees}},
-url = {http://doi.wiley.com/10.1111/j.1365-2745.2008.01445.x},
-volume = {97},
-year = {2009}
-}
-@book{Ripley1981,
-address = {Hoboken, New Jersey},
-author = {Ripley, Brian D.},
-booktitle = {Wiley Series in Probability and Mathematical Statistics},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1981 - Spatial statistics.pdf:pdf},
-isbn = {9780471691167},
-publisher = {John Wiley {\&} Sons},
-title = {{Spatial statistics}},
-year = {1981}
-}
-@article{Westoby2002,
-abstract = {Abstract An important aim of plant ecology is to identify leading dimensions of ecological variation among species and to understand the basis for them. Dimensions that can readily be measured would be especially useful, because they might offer a path towards improved worldwide synthesis across the thousands of field experiments and ecophysiological studies that use just a few species each. Four dimensions are reviewed here. The leaf mass per area-leaf lifespan (LMA-LL) dimension expresses slow turnover of plant parts (at high LMA and long LL), long nutrient residence times, and slow response to favorable growth conditions. The seed mass-seed output (SM-SO) dimension is an important predictor of dispersal to establishment opportunities (seed output) and of establishment success in the face of hazards (seed mass). The LMA-LL and SM-SO dimensions are each underpinned by a single, comprehensible tradeoff, and their consequences are fairly well understood. The leaf size-twig size (LS-TS) spectrum has obvious consequences for the texture of canopies, but the costs and benefits of large versus small leaf and twig size are poorly understood. The height dimension has universally been seen as ecologically important and included in ecological strategy schemes. Nevertheless, height includes several tradeoffs and adaptive elements, which ideally should be treated separately. Each of these four dimensions varies at the scales of climate zones and of site types within landscapes. This variation can be interpreted as adaptation to the physical environment. Each dimension also varies widely among coexisting species. Most likely this within-site variation arises because the ecological opportunities for each species depend strongly on which other species are present, in other words, because the set of species at a site is a stable mixture of strategies.},
-author = {Westoby, Mark and Falster, Daniel S. and Moles, Angela T. and Vesk, Peter A. and Wright, Ian J.},
-doi = {10.1146/annurev.ecolsys.33.010802.150452},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Westoby et al. - 2002 - PLANT ECOLOGICAL STRATEGIES Some Leading Dimensions of Variation Between Species.pdf:pdf},
-journal = {Annual Review of Ecology and Systematics},
-number = {1},
-pages = {125--159},
-title = {{PLANT ECOLOGICAL STRATEGIES: Some Leading Dimensions of Variation Between Species}},
-url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150452?journalCode=ecolsys.1},
-volume = {33},
-year = {2002}
-}
-@article{Mouchet2008,
-abstract = {The widely used FD index of functional diversity is based on the construction of a dendrogram. This index has been the subject of a strong debate concerning the choice of the distance and the clustering method to be used, since the method chosen may greatly affect the FD values obtained. Much of this debate has been centred around which method of dendrogram construction gives a faithful representation of species distribution in multidimensional functional trait space. From artificially generated datasets varying in species richness and correlations between traits, we test whether any single combination of clustering method(s) and distance consistently produces a dendrogram that most closely corresponds to the matrix of functional distances between pairs of species studied. We also test the ability of consensus trees, which incorporate features common to a range of different dendrograms, to summarize distance matrices. Our results show that no combination of clustering method(s) and distance constantly outperforms the others due to the complexity of interactions between correlations of traits, species richness, distance measures and clustering methods. Furthermore, the construction of a consensus tree from a range of dendrograms is often the best solution. Consequently, we recommend testing all combinations of distances and clustering methods (including consensus trees), then selecting the most reliable tree (with the lowest dissimilarity) to estimate FD value. Furthermore we suggest that any index that requires the construction of functional dendrograms potentially benefits from this new approach. Functio},
-author = {Mouchet, Maud A. and Guilhaumon, Fran{\c{c}}ois and Vill{\'{e}}ger, S{\'{e}}bastien and Mason, Norman W. H. and Tomasini, Jean-Antoine and Mouillot, David},
-doi = {10.1111/j.0030-1299.2008.16594.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mouchet et al. - 2008 - Towards a consensus for calculating dendrogram-based functional diversity indices.pdf:pdf},
-journal = {Oikos},
-pages = {794--800},
-title = {{Towards a consensus for calculating dendrogram-based functional diversity indices}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0030-1299.2008.16594.x/abstract},
-volume = {117},
-year = {2008}
-}
-@book{Clarke1976,
-address = {Cambridge},
-author = {Clarke, David L.},
-pages = {1--270},
-publisher = {Cambridge University Press},
-title = {{New Studies in Archaeology}},
-year = {1976}
-}
-@article{Raaijmakers1987,
-abstract = {An application of the method of maximum likelihood (ML) is described for analysing the results of enzyme kinetic experiments in which the Michaelis-Menten equation is obeyed. Accurate approximate solutions to the ML equations for the parameter estimates are presented for the case in which the experimental errors are of constant relative magnitude. Formulae are derived that approximate the standard errors of these estimates. The estimators are shown to be asymptotically unbiased and the standard errors observed in simulated data rapidly approach the theoretical lower bound as the sample size increases. The results of a large-scale Monte Carlo simulation study indicate that for data with a constant coefficient of variation, the present method is superior to other published methods, including the conventional transformations to linearity and the nonparametric technique proposed by Eisenthal and Cornish-Bowden (1974, Biochemical Journalt39, 715-720). Finally, the present results are extended to the analysis of simple receptor binding experiments using the general approach described by Munson and Rodbard (1980, Analytical Biochemistry 107, 220-239).},
-author = {Raaijmakers, Jeroen G. W.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Raaijmakers - 1987 - Statistical Analysis of the Michaelis-Menten Equation.pdf:pdf},
-journal = {Biometrics},
-number = {4},
-pages = {793--803},
-title = {{Statistical Analysis of the Michaelis-Menten Equation}},
-volume = {43},
-year = {1987}
-}
-@article{Suyari2004,
-abstract = {Tsallis entropy, one-parameter generalization of Shannon entropy, has been often discussed in statistical physics as a new information measure. This new information measure has provided many satisfactory physical interpretations in nonextensive systems exhibiting chaos or fractal. We present the generalized Shannon-Khinchin axioms to nonextensive systems and prove the uniqueness theorem rigorously. Our results show that Tsallis entropy is the simplest among all nonextensive entropies. By the detailed comparisons of our axioms with the previously presented two sets of axioms, we reveal the peculiarity of pseudoadditivity as an axiom. In this correspondence, the most fundamental basis for Tsallis entropy as information measure is established in the information-theoretic framework.},
-author = {Suyari, Hiroki},
-doi = {10.1109/TIT.2004.831749},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Suyari - 2004 - Generalization of Shannon – Khinchin Axioms to the Nonextensive Entropy.pdf:pdf},
-journal = {IEEE Transactions on Information Theory},
-number = {8},
-pages = {1783--1787},
-title = {{Generalization of Shannon – Khinchin Axioms to the Nonextensive Entropy}},
-volume = {50},
-year = {2004}
-}
-@article{Pavoine2005a,
-abstract = {In this paper, we introduce the concept of ?originality of a species within a set? in order to indicate the average rarity of all the features belonging to this species. Using a phylogenetic tree of 70 species of New World terrestrial Carnivora, we suggest measuring the originality by a probability distribution. This maximizes the expected number of features shared by two species randomly drawn from the set. By using this new index, we take account of branch lengths whereas current indices of originality focus on tree topology. As a supplement to Nee and May's optimizing algorithm, we find that originality must be one of the criteria used in conservation planning. Keywords},
-author = {Pavoine, Sandrine and Ollier, S{\'{e}}bastien and Dufour, Anne-B{\'{e}}atrice},
-doi = {10.1111/j.1461-0248.2005.00752.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Ollier, Dufour - 2005 - Is the originality of a species measurable.pdf:pdf},
-journal = {Ecology Letters},
-pages = {579--586},
-title = {{Is the originality of a species measurable?}},
-volume = {8},
-year = {2005}
-}
-@phdthesis{Collinet1997,
-address = {Lyon},
-author = {Collinet, Fr{\'{e}}d{\'{e}}rique},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Collinet - 1997 - Essai de regroupement des principales esp{\`{e}}ces structurantes d'une for{\^{e}}t dense humide d'apr{\`{e}}s leur r{\'{e}}partition spatiale.pdf:pdf},
-school = {Universit{\'{e}} Claude Bernard, Lyon I},
-title = {{Essai de regroupement des principales esp{\`{e}}ces structurantes d'une for{\^{e}}t dense humide d'apr{\`{e}}s leur r{\'{e}}partition spatiale (for{\^{e}}t de Paracou, Guyane)}},
-year = {1997}
-}
-@article{Guimaraes1998,
-abstract = {This study uses nested logit to estimate the influence of industrial incentives on the location of manufacturing plants in Puerto Rico. Puerto Rican laws grant generous tax exemptions and provide other incentives for investments in less-developed, peripheral regions of the island. Focusing on Puerto Rico allowed us to isolate and test location factors in a closed environment where 76 municipalities received a development zone designation and competed directly against one another for new plants. Simulations indicated that the regional incentive policy reallocated relatively few of the greenfield investments from the congested core to the periphery of the island.},
-author = {Guimar{\~{a}}es, Paulo and Rolfe, Robert J. and Woodward, Douglas P.},
-doi = {10.1177/016001769802100202},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guimar{\~{a}}es, Rolfe, Woodward - 1998 - Regional Incentives and Industrial Location in Puerto Rico.pdf:pdf},
-journal = {International Regional Science Review},
-number = {2},
-pages = {119--138},
-title = {{Regional Incentives and Industrial Location in Puerto Rico}},
-url = {http://journals.sagepub.com/doi/abs/10.1177/016001769802100202},
-volume = {21},
-year = {1998}
-}
-@article{Pavoine2005,
-abstract = {Many methods that study the diversity within hierarchically structured populations have been developed in genetics. Among them, the analysis of molecular variance (AMOVA) (Excoffier et al., 1992) has the advantage of including evolutionary distances between individuals. AMOVA is a special case of a far more general statistical scheme produced by Rao (1982a; 1986) and called the apportionment of quadratic entropy (APQE). It links diversity and dissimilarity and allows the decomposition of diversity according to a given hierarchy. We apply this framework to ecological data showing that APQE may be very useful for studying diversity at various spatial scales. Moreover, the quadratic entropy has a critical advantage over usual diversity indices because it takes into account differences between species. Finally, the differences that can be incorporated in APQE may be either taxonomic or functional ( biological traits), which may be of critical interest for ecologists.},
-author = {Pavoine, Sandrine and Doledec, Sylvain},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Doledec - 2005 - The apportionment of quadratic entropy a useful alternative for partitioning diversity in ecological data.pdf:pdf},
-isbn = {1352-8505},
-journal = {Environmental and Ecological Statistics},
-number = {2},
-pages = {125--138},
-title = {{The apportionment of quadratic entropy: a useful alternative for partitioning diversity in ecological data}},
-volume = {12},
-year = {2005}
-}
-@article{Lingoes1971,
-abstract = {This paper gives a rigorous and greatly simplified proof of Guttman's theorem for the least upper-bound dimensionality of arbitrary real symmetric matrices S, where the points embedded in a real Euclidean space subtend distances which are strictly monotone with the off-diagonal elements ofS. A comparable and more easily proven theorem for the vector model is also introduced. At most, n-2 dimensions are required to reproduce the order information for both the distance and vector models and this is true for any choice of real indices, whether they define a metric space or not. If ties exist in the matrices to be analyzed, then greatest lower bounds are specifiable when degenerate solutions are to be avoided. These theorems have relevance to current developments in nonmetric techniques for the monotone analysis of data matrices.},
-author = {Lingoes, James C.},
-doi = {10.1007/BF02291398},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lingoes - 1971 - Some boundary conditions for a monotone analysis of symmetric matrices.pdf:pdf},
-journal = {Psychometrika},
-number = {2},
-pages = {195--203},
-title = {{Some boundary conditions for a monotone analysis of symmetric matrices}},
-url = {http://link.springer.com/article/10.1007/BF02291398},
-volume = {36},
-year = {1971}
-}
-@article{Kempton1974,
-author = {Kempton, R. A. and Taylor, L. R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kempton, Taylor - 1974 - Log-series and log-normal parameters as diversity discriminators for Lepidoptera.pdf:pdf},
-journal = {Journal of Animal Ecology},
-number = {2},
-pages = {381--399},
-title = {{Log-series and log-normal parameters as diversity discriminators for Lepidoptera}},
-volume = {43},
-year = {1974}
-}
-@article{Hui2014,
-abstract = {Patterns in species incidence and compositional turnover are central to understanding what drives biodiversity. Here we propose zeta (z) diversity, the number of species shared by multiple assemblages, as a concept and metric that unifies incidence-based diversity measures, patterns, and relationships. Unlike other mea- sures of species compositional turnover, zeta diversity partitioning quantifies the complete set of diversity components for multiple assemblages, comprehensively representing the spatial structure of multispecies distributions. To illustrate the application and ecological value of zeta diversity, we show how it scales with sample number, grain, and distance. Zeta diversity reconciles several different bio- diversity patterns, including the species accumulation curve, the species-area relationship, multispecies occupancy patterns, and scaling of species endemism. Exponential and power-law forms of zeta diversity are associated with stochastic versus niche assembly processes. Zeta diversity may provide new insights on biodiversity patterns, the processes driving them, and their response to environmental change.},
-author = {Hui, Cang and McGeoch, Melodie A.},
-doi = {10.1086/678125},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hui, McGeoch - 2014 - Zeta Diversity as a Concept and Metric That Unifies Incidence-Based Biodiversity Patterns.pdf:pdf},
-journal = {The American Naturalist},
-number = {5},
-pages = {684--694},
-title = {{Zeta Diversity as a Concept and Metric That Unifies Incidence-Based Biodiversity Patterns}},
-url = {http://www.jstor.org/stable/info/10.1086/678125},
-volume = {184},
-year = {2014}
-}
-@article{Ludovisi2006,
-abstract = {Since its introduction in the early 1950s, information theory, thanks to the link among the concepts of information, entropy and complexity, has seemed to provide a theoretical basis and statistical tools for capturing some of the fundamental properties of complex living systems from the molecular to the community scale. Moreover, the flexibility of information analysis, which resides essentially in the fact that its applicability is not burdened by restrictive assumptions on the underlying probability distribution of data, which characterise conventional multivariate statistics, has facilitated its widespread use among biologists. In spite of their common root with Shannon's H', which is probably the most widely used index of alpha diversity in ecology, the Kullback-Leibler information measures have received scant attention from ecologists as dissimilarity measures between communities. In this paper, after having illustrated the potentiality of applying them to this matter, we propose a similarity index based on the Kullback-Leibler divergence and on the concept of sample coverage, and test its effectiveness by applying it to the evaluation of beta diversity of phytoplankton along a water stability gradient in Lake Trasimeno (Umbria, Italy). The results show that the proposed indices are effective in revealing a community gradient which is consistent with the environmental gradient investigated and advise their use particularly when there are slight differences in the composition and structure of the communities being compared. The study also shows how the decomposition of the divergence function can offer a way for calculating and partitioning the total diversity of a pooled set of communities from the perspective of information theory.},
-annote = {doi: DOI: 10.1016/j.ecolmodel.2005.05.022},
-author = {Ludovisi, Alessandro and Taticchi, Maria Illuminata},
-doi = {10.1016/j.ecolmodel.2005.05.022},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ludovisi, Taticchi - 2006 - Investigating beta diversity by Kullback-Leibler information measures.pdf:pdf},
-journal = {Ecological Modelling},
-number = {1-2},
-pages = {299--313},
-title = {{Investigating beta diversity by Kullback-Leibler information measures}},
-url = {http://www.sciencedirect.com/science/article/B6VBS-4GP1VRK-1/2/6546ebdfe79445ef3684e0bf8dec9d14},
-volume = {192},
-year = {2006}
-}
-@book{Weber1909,
-author = {Weber, Alfred},
-publisher = {T{\"{u}}bingen. English translation edited in 1971, "Theory of the location of industries", Russell {\&} Russell.},
-title = {{{\"{U}}ber den Standort der Industrien}},
-year = {1909}
-}
-@article{Pavoine2011,
-abstract = {One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large-scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large-scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global-scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within-species variations.},
-author = {Pavoine, Sandrine and Bonsall, Michael B.},
-doi = {10.1111/j.1469-185X.2010.00171.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Bonsall - 2011 - Measuring biodiversity to explain community assembly a unified approach.pdf:pdf},
-journal = {Biological Reviews},
-number = {4},
-pages = {792--812},
-title = {{Measuring biodiversity to explain community assembly: a unified approach}},
-url = {http://dx.doi.org/10.1111/j.1469-185X.2010.00171.x},
-volume = {86},
-year = {2011}
-}
-@article{Chave2007a,
-abstract = {To predict how ecological communities respond to large-scale patterns of fragmentation, both local and global processes need to be combined into an integrated modelling approach. Using neotropical rain forests as an illustration, we constructed a large metacommunity (200 km × 200 km) where all the trees ≥ 10 cm dbh are modelled, assuming panmixis within local communities (each 10 km × 10 km in size), and limited dispersal across communities. Under the assumption of neutrality, we simulated an equilibrium configuration, that we subsequently submitted to several scenarios of environmental fragmentation. Fragmentation leads to a significant reduction of species diversity in edge communities. After the disturbance, the system returns to equilibrium rapidly if the disturbance is not too widespread, due to dispersal from neighboring areas. However, post-disturbance levels of local diversity remain much lower that pre-disturbance ones, at least within ecological times. These results illustrate the claim that neutral landscape models exhibit a partly predictable ecological-time dynamics, mostly driven by the ability of the metacommunity to buffer accidents in local communities. Such a multi-scale model should be considered as a null scenario in testing more complex effects related to habitat fragmentation, such as genetic bottlenecks, or loss of keystone species. {\textcopyright} 2007 Elsevier B.V. All rights reserved.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Norden, Natalia},
-doi = {10.1016/j.ecolmodel.2007.03.025},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave, Norden - 2007 - Changes of species diversity in a simulated fragmented neutral landscape.pdf:pdf},
-journal = {Ecological Modelling},
-number = {1},
-pages = {3--10},
-title = {{Changes of species diversity in a simulated fragmented neutral landscape}},
-volume = {207},
-year = {2007}
-}
-@misc{Oksanen2012,
-author = {Oksanen, Jari and Blanchet, F. Guillaume and Kindt, Roeland and Legendre, Pierre and Minchin, Peter R. and O'Hara, R. B. and Simpson, Gavin L. and Solymos, Peter and Stevens, M. Henry H. and Wagner, Helene},
-title = {{vegan: Community Ecology Package}},
-url = {http://cran.r-project.org/package=vegan},
-year = {2012}
-}
-@article{Tucker2016,
-abstract = {The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriatemetric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information.},
-author = {Tucker, Caroline M. and Cadotte, Marc W. and Carvalho, Silvia B. and Davies, T. Jonathan and Ferrier, Simon and Fritz, Susanne A. and Grenyer, Rich and Helmus, Matthew R. and Jin, Lanna S. and Mooers, Arne {\O}. and Pavoine, Sandrine and Purschke, Oliver and Redding, David W. and Rosauer, Dan F. and Winter, Marten and Mazel, Florent},
-doi = {10.1111/brv.12252},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tucker et al. - 2016 - A guide to phylogenetic metrics for conservation, community ecology and macroecology.pdf:pdf},
-journal = {Biological Reviews},
-title = {{A guide to phylogenetic metrics for conservation, community ecology and macroecology}},
-url = {http://doi.wiley.com/10.1111/brv.12252},
-volume = {in press},
-year = {2016}
-}
-@article{Real1996,
-abstract = {An individual host's likelihood of acquiring an infectious disease depends, in large part, on the location of the host relative to sources of infection, proximity to other hosts, and occupation of specific microhabitats that confer increased susceptibility. Spatial organization of the host and pathogen populations then may be critical in determining patterns of disease occurrence and dynamics. We discuss three fundamental problems associated with understanding the interactions of plants, pathogens, and spatial structure: (1) how one characterizes spatial patterns, (2) how we determine spatial dynamic processes from a given spatial pattern, and (3) how we then simulate the spatial dynamics presumed to be dominating a given host-pathogen interaction. To demonstrate methods for the characterization of spatial pattern, we analyzed spatial maps of a Silene latifolia population infected with the anther smut Microbotryum violaceum, using join-count statistics, continuous spatial autocorrelation, and Mantel's test. Different statistical techniques provided different interpretations of the same data set, indicating the value of using multiple methods. We described spatial structure in the plant population, the pathogen population (factoring out the plant population structure), and spatial cross correlation between two variables (plant gender and disease status). Each of these tests provides information on how the disease may be spreading in the population. We are not very optimistic about the prospect of determining underlying disease-spread processes purely from analysis of spatial pattern. Most spatial patterns can potentially be generated by a number of biological processes (e.g., “true” vs. “apparent” contagion), and it is not possible to distinguish between hypotheses without additional information about the system. A difficulty in modeling spatial processes is simulation of populations with given spatial patterns. Simulated spatially structured populations are useful for predicting disease dynamics in a spatial context. We present a number of techniques for creating these spatially structured populations, including a method we developed for modeling the effect of vector behavior on the spread of a plant virus.},
-author = {Real, Leslie A. and McElhany, Paul},
-doi = {10.2307/2265572},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Real, McElhany - 1996 - Spatial Pattern and Process in Plant-Pathogen Interactions.pdf:pdf},
-journal = {Ecology},
-number = {4},
-pages = {1011--1025},
-title = {{Spatial Pattern and Process in Plant-Pathogen Interactions}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/2265572/full},
-volume = {77},
-year = {1996}
-}
-@article{Baez2011,
-abstract = {There are numerous characterizations of Shannon entropy and Tsallis entropy as measures of information obeying certain properties. Using work by Faddeev and Furuichi, we derive a very simple characterization. Instead of focusing on the entropy of a probability measure on a finite set, this characterization focuses on the "information loss", or change in entropy, associated with a measure-preserving function. Information loss is a special case of conditional entropy: namely, it is the entropy of a random variable conditioned on some function of that variable. We show that Shannon entropy gives the only concept of information loss that is functorial, convex-linear and continuous. This characterization naturally generalizes to Tsallis entropy as well.},
-annote = {Cited By (since 1996):1
-Export Date: 12 December 2013
-Source: Scopus},
-author = {Baez, John C. and Fritz, Tobias and Leinster, Tom},
-doi = {10.3390/e13111945},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baez, Fritz, Leinster - 2011 - A characterization of entropy in terms of information loss.pdf:pdf},
-journal = {Entropy},
-number = {11},
-pages = {1945--1957},
-title = {{A characterization of entropy in terms of information loss}},
-url = {http://www.mdpi.com/1099-4300/13/11/1945},
-volume = {13},
-year = {2011}
-}
-@misc{Maechler2014,
-author = {Maechler, M. and Rousseeuw, P. and Struyf, A. and Hubert, M. and Hornik, K.},
-title = {{cluster: Cluster Analysis Basics and Extensions}},
-url = {http://cran.r-project.org/package=cluster},
-year = {2014}
-}
-@article{Cardoso2014,
-abstract = {Aim: To propose a unified framework for quantifying taxon (T$\beta$), phylogenetic (P$\beta$) and functional (F$\beta$) beta diversity via pairwise comparisons of communities, which allows these types of beta diversity to be partitioned into ecologically meaningful additive components. Location: Global, with case studies in Europe and the Azores archipelago. Methods: Using trees as a common representation for taxon, phylogenetic and functional diversity, we partition total beta diversity ($\beta$total) into its replacement (turnover, $\beta$repl) and richness difference ($\beta$rich) components according to which part of a global tree was shared by or unique to communities that were being compared. We demonstrate the application of this framework using artificial and empirical examples (mammals in Europe and epigean arthropods in the Azores). Results: Our empirical examples show that comparing P$\beta$ and F$\beta$ with the most commonly used T$\beta$ revealed previously hidden patterns of beta diversity. More importantly, we demonstrate that partitioning P$\beta$total and F$\beta$total into their respective $\beta$repl and $\beta$rich components facilitates the detection of more complex patterns than using the overall coefficients alone, further elucidating the different forces operating in community assembly.$\backslash$n$\backslash$n$\backslash$nMain conclusions$\backslash$n$\backslash$nThe methods presented here allow the integration and full comparison of T$\beta$, P$\beta$ and F$\beta$. They provide a tool for effectively disentangling the replacement (turnover) and richness difference components of the different biodiversity facets within the same methodological framework.},
-author = {Cardoso, Pedro and Rigal, Fran{\c{c}}ois and Carvalho, Jos{\'{e}} C. and Fortelius, Mikael and Borges, Paulo A. V. and Podani, J{\'{a}}nos and Schmera, D{\'{e}}nes},
-doi = {10.1111/jbi.12239},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cardoso et al. - 2014 - Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference componen.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {4},
-pages = {749--761},
-title = {{Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components}},
-volume = {41},
-year = {2014}
-}
-@article{Acs1988,
-abstract = {We present a model suggesting that innovative output is influenced by R{\&}D and market structure characteristics. Based on a new and direct measure of innova- tion, we find that (1) the total number of innovations is negatively related to concentration and unionization, and positively related to R{\&}D, skilled labor, and the degree to which large firms comprise the industry; and (2) these determinants have disparate effects on large and small firms.},
-author = {Acs, Zoltan J. and Audretsch, David B.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Acs, Audretsch - 1988 - Innovation in Large and Small Firms An Empirical Analysis.pdf:pdf},
-journal = {The American Economic Review},
-number = {4},
-pages = {678--690},
-title = {{Innovation in Large and Small Firms: An Empirical Analysis}},
-url = {http://www.jstor.org/stable/1811167},
-volume = {78},
-year = {1988}
-}
-@article{Chave2004a,
-abstract = {The above-ground biomass (AGB) of tropical forests is a crucial variable for ecologists, biogeochemists, foresters and policymakers. Tree inventories are an efficient way of assessing forest carbon stocks and emissions to the atmosphere during deforestation. To make correct inferences about long-term changes in biomass stocks, it is essential to know the uncertainty associated with AGB estimates, yet this uncertainty is rarely evaluated carefully. Here, we quantify four types of uncertainty that could lead to statistical error in AGB estimates: (i) error due to tree measurement; (ii) error due to the choice of an allometric model relating AGB to other tree dimensions; (iii) sampling uncertainty, related to the size of the study plot(iv) representativeness of a network of small plots across a vast forest landscape. In previous studies, these sources of error were reported but rarely integrated into a consistent framework. We estimate all four terms in a 50 hectare (ha, where 1 ha = 10(4) m(2)) plot on Barro Colorado Island, Panama, and in a network of 1 ha plots scattered across central Panama. We find that the most important source of error is currently related to the choice of the allometric model. More work should be devoted to improving the predictive power of allometric models for biomass.},
-author = {Chave, J{\'{e}}r{\^{o}}me and Condit, Richard and Aguilar, Salom{\'{o}}n and Hernandez, Andres and Lao, Suzanne and Perez, Rolando},
-doi = {10.1098/rstb.2003.1425},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chave et al. - 2004 - Error propagation and scaling for tropical forest biomass estimates.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1443},
-pages = {409--420},
-title = {{Error propagation and scaling for tropical forest biomass estimates}},
-volume = {359},
-year = {2004}
-}
-@article{Novak1992,
-abstract = {A measure of macroinvertebrate community composition was developed using data from 46 shallow freshwater streams in New York State. It is intended for use in conjunction with other biological indices to assess water quality. Using unpolluted sites selected from 300 kick samples, an ideal community composition was developed and expressed as percent composition of seven major organism groups. The index of percentage similarity, as developed by Whittaker and Fairbanks (1958, Ecology 39:46-65), is used to measure the affinity of a community in a sampled riffle to that of the expected model community. Percent model affinity was found to be closely correlated with the Hilsenhoff Biotic Index (HBI) and the species richness of Ephemeroptera, Plecoptera, and Tri- choptera, and reflected water quality changes better than HBI did in instances of non-organic pollution. With modification of the model community abundances, this measure has potential for use in other geographic areas},
-author = {Novak, M. A. and Bode, R. W.},
-doi = {10.2307/1467884},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Novak, Bode - 1992 - Percent Model Affinity A New Measure of Macroinvertebrate Community Composition Percent model affinity a new meas.pdf:pdf},
-journal = {Journal of the North American Benthological Society},
-number = {1},
-pages = {80--85},
-title = {{Percent Model Affinity: A New Measure of Macroinvertebrate Community Composition}},
-url = {http://www.jstor.org/stable/1467884},
-volume = {11},
-year = {1992}
-}
-@article{Bikhchandani1998,
-author = {Bikhchandani, Sushil and Hirshleifer, David and Welch, Ivo},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bikhchandani, Hirshleifer, Welch - 1998 - Learning from the Behavior of Others Conformity, Fads, and Informational Cascades.pdf:pdf},
-journal = {Journal of Economic Perspectives},
-number = {3},
-pages = {151--170},
-title = {{Learning from the Behavior of Others: Conformity, Fads, and Informational Cascades}},
-url = {http://www.jstor.org/stable/2647037},
-volume = {12},
-year = {1998}
-}
-@article{Dornelas2013,
-abstract = {Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series-lack of physical boundaries, uni-dimensionality, autocorrelation and directionality-that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.},
-annote = {ISI Document Delivery No.: 048WE
-Times Cited: 1
-Cited Reference Count: 86
-Dornelas, Maria Magurran, Anne E. Buckland, Stephen T. Chao, Anne Chazdon, Robin L. Colwell, Robert K. Curtis, Tom Gaston, Kevin J. Gotelli, Nicholas J. Kosnik, Matthew A. McGill, Brian McCune, Jenny L. Morlon, Helene Mumby, Peter J. Ovreas, Lise Studeny, Angelika Vellend, Mark
-European Research Council [BioTIME 250189]
-This paper is the result of a meeting held at the Royal Society International Kavli Centre. We thank Jonathan Chase, John Alroy, Jan Bengtson, Miguel Barbosa and Al Reeve for comments on previous versions of this manuscript. A.E.M. and M.D. acknowledge the European Research Council (project BioTIME 250189) for support.
-Royal soc
-London},
-author = {Dornelas, Maria and Magurran, Anne E. and Buckland, Stephen T. and Chao, Anne and Chazdon, Robin L. and Colwell, Robert K. and Curtis, Tom and Gaston, Kevin J. and Gotelli, Nicholas J. and Kosnik, Matthew A. and McGill, Brian and McCune, Jenny L. and Morlon, H{\'{e}}l{\`{e}}ne and Mumby, Peter J. and {\O}vre{\aa}s, Lise and Studeny, Angeli and Vellend, Mark},
-doi = {10.1098/rspb.2012.1931},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Dornelas et al. - 2013 - Quantifying temporal change in biodiversity challenges and opportunities.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {20121931},
-title = {{Quantifying temporal change in biodiversity: challenges and opportunities}},
-url = {http://rspb.royalsocietypublishing.org/content/280/1750/20121931.full.pdf},
-volume = {280},
-year = {2013}
-}
-@article{Alatalo1981,
-abstract = {Evenness is considered as the measure of equality of abundances in a community. By comparing artificial abundance distributions the modified Hill's ratio (N,- l)I(N ,- 1) was found to be the most easily interpreted evenness measure. The modification (subtracting 1 from Hill's numbers) is important when species diversity is low. Often the species richness of the community is underestimated, and because of the sampling bias evenness indices not using species richness are recommendable. The most popular evenness index J' seems to be a rather ambiguous measure, since it is for purely mathematical reasons positively correlated with species richness. The ambiguity arises from the logarithmic relation of Shannon's entropy H' to species richness. Hill's numbers with species as units are less ambiguous than diversity meas- ures in general. After all, it is emphasized that there is no single way to measure evenness, and because of the looseness of the concept we have to be cautious in its application.},
-author = {Alatalo, Rauno V.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alatalo - 1981 - Problems in the Measurement of Evenness in Ecology.pdf:pdf},
-journal = {Oikos},
-number = {2},
-pages = {199--204},
-title = {{Problems in the Measurement of Evenness in Ecology}},
-volume = {37},
-year = {1981}
-}
-@article{Ellison1999,
-author = {Ellison, Glenn and Glaeser, Edward L},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ellison, Glaeser - 1999 - The Geographic Concentration of Industry Does Natural Advantage Explain Agglomeration.pdf:pdf},
-journal = {The American Economic Review},
-number = {2},
-pages = {311--316},
-title = {{The Geographic Concentration of Industry: Does Natural Advantage Explain Agglomeration?}},
-url = {https://www.jstor.org/stable/117127},
-volume = {89},
-year = {1999}
-}
-@article{Hurka1983,
-annote = {La citation de St Thomas d'Aquin est fausse.},
-author = {Hurka, Thomas},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hurka - 1983 - Value and Population Size.pdf:pdf},
-journal = {Ethics,},
-number = {3},
-pages = {496--507},
-title = {{Value and Population Size}},
-volume = {93},
-year = {1983}
-}
-@phdthesis{Favrichon1995,
-address = {Lyon},
-author = {Favrichon, Vincent},
-school = {Universit{\'{e}} Claude Bernard, Lyon I},
-title = {{Mod{\`{e}}le matriciel d{\'{e}}terministe en temps discret : Application {\`{a}} l'{\'{e}}tude de la dynamique d'un peuplement forestier tropical humide (Guyane Fran{\c{c}}aise)}},
-year = {1995}
-}
-@article{Heckman1979,
-author = {Heckman, James J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Heckman - 1979 - Sample Selection Bias as a Specification Error.pdf:pdf},
-journal = {Econometrica},
-keywords = {Heckman (1979).pdf},
-mendeley-tags = {Heckman (1979).pdf},
-number = {1},
-pages = {153--162},
-title = {{Sample Selection Bias as a Specification Error}},
-volume = {47},
-year = {1979}
-}
-@article{Stoyan2000,
-abstract = {Forestry statistics is an important field of applied statistics with a long tradition. Many forestry problems can be solved by means of point processes or marked point processes. There, the "points" are tree locations and the "marks" are tree characteristics such as diameter at breast height or degree of damage by environmental. factors. Point process characteristics are valuable tools for exploratory data analysis in forestry, for describing the variability of forest stands and for understanding and quantifying ecological relationships. Models of point processes are also an important basis of modern single-tree modeling, that gives simulation tools for the investigation of forest structures and for the prediction of results of forestry operations such as plantation and thinning.},
-author = {Stoyan, Dietrich and Penttinen, Antti},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan, Penttinen - 2000 - Recent applications of point process methods in forestry statistics.pdf:pdf},
-journal = {Statistical Science},
-number = {1},
-pages = {61--78},
-title = {{Recent applications of point process methods in forestry statistics}},
-url = {http://www.jstor.org/stable/2676677},
-volume = {15},
-year = {2000}
-}
-@article{Letcher2012,
-abstract = {The phylogenetic structure of communities can reveal forces shaping community assembly, but the vast majority of work on phylogenetic community structure has been conducted in mature ecosystems. Here, we present an analysis of the phylogenetic structure of three Neotropical rain forest communities undergoing succession. In each site, the net relatedness of the community is initially high and consistently declines during succession. This pattern is evident both when comparing plots of different age classes and when comparing stem size classes within each plot: the oldest plots and the youngest stem cohorts, representing the most advanced stages of succession, have the lowest relatedness. Our results suggest that succession leaves a distinct signature in the phylogenetic structure of communities, which may reflect an increasing role of biotic interactions in community assembly during succession. We discuss theoretical explanations for the decline in community phylogenetic relatedness during succession, and suggest directions for future study. {\textcopyright} 2011 Perspectives in Plant Ecology, Evolution and Systematics.},
-author = {Letcher, Susan G. and Chazdon, Robin L. and Andrade, Ana C. S. and Bongers, Frans and van Breugel, Michiel and Finegan, Bryan and Laurance, Susan G. and Mesquita, Rita C. G. and Mart{\'{i}}nez-Ramos, Miguel and Williamson, G. Bruce},
-doi = {10.1016/j.ppees.2011.09.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Letcher et al. - 2012 - Phylogenetic community structure during succession Evidence from three Neotropical forest sites.pdf:pdf},
-journal = {Perspectives in Plant Ecology, Evolution and Systematics},
-number = {2},
-pages = {79--87},
-title = {{Phylogenetic community structure during succession: Evidence from three Neotropical forest sites}},
-url = {http://dx.doi.org/10.1016/j.ppees.2011.09.005},
-volume = {14},
-year = {2012}
-}
-@article{Lande2000,
-abstract = {Diversity in biological communities frequently is compared using species accumulation curves, plotting observed species richness versus sample size. When species accumulation curves intersect, the ranking of communities by observed species richness depends on sample size, creating inconsistency in comparisons of diver- sity. We show that species accumulation curves for two commu- nities are expected to intersect when the community with lower actual species richness has higher Simpson diversity (probability that two random individuals belong to different species). This may often occur when comparing communities that differ in habitat heterogeneity or disturbance, as we illustrate using data from neotropical butterflies. In contrast to observed species richness, estimated Simpson diversity always produces a consis- tent expected ranking among communities across sample sizes, with the statistical accuracy to confidently rank communities using small samples. Simpson diversity should therefore be par- ticularly useful in rapid assessments to prioritize areas for conservation.},
-author = {Lande, Russell and DeVries, Philip J. and Walla, Thomas R.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lande, DeVries, Walla - 2000 - When species accumulation curves intersect implications for ranking diversity using small samples.pdf:pdf},
-journal = {Oikos},
-number = {3},
-pages = {601--605},
-title = {{When species accumulation curves intersect: implications for ranking diversity using small samples}},
-volume = {89},
-year = {2000}
-}
-@article{Solow1993,
-abstract = {In optimizing strategies aimed at the conservation of biological diversity, it is necessary to compare the consequences of competing strategies for biological diversity. This paper presents a general approach to this problem. An example concerning the conservation of crane species is given.},
-author = {Solow, Andrew and Polasky, Stephen and Broadus, James},
-doi = {10.1016/S0003-9861(71)80064-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Solow, Polasky, Broadus - 1993 - On the Measurement of Biological Diversity.pdf:pdf},
-journal = {Archives of biochemistry and biophysics},
-pages = {60--68},
-title = {{On the Measurement of Biological Diversity}},
-url = {http://www.sciencedirect.com/science/article/pii/S0095069683710041},
-volume = {24},
-year = {1993}
-}
-@article{Barrios2009,
-abstract = {Barrios S., Bertinelli L., Strobl E. and Teixeira A. C. Spatial distribution of manufacturing activity and its determinants: a comparison of three small European countries, Regional Studies. The paper investigates and compares the spatial distribution of manufacturing activity and its determinants in Belgium, Ireland, and Portugal using comparable, exhaustive micro-level data sets. Some similarities are found between Portugal and Belgium, but little for Ireland. Moreover, there is some evidence that forward and backward linkages, research and development activity, and labour market pooling of skilled labour can be important determinants of agglomeration, although this crucially depends on the country examined.},
-annote = {454AU
-Times Cited:3
-Cited References Count:51},
-author = {Barrios, Salvador and Bertinelli, Luisito and Strobl, Eric and Teixeira, Antonio Carlos},
-doi = {10.1080/00343400801922822},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barrios et al. - 2009 - Spatial Distribution of Manufacturing Activity and its Determinants A Comparison of Three Small European Coun(2).pdf:pdf},
-journal = {Regional Studies},
-number = {5},
-pages = {721--738},
-title = {{Spatial Distribution of Manufacturing Activity and its Determinants: A Comparison of Three Small European Countries}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/00343400801922822},
-volume = {43},
-year = {2009}
-}
-@article{Madelaine2007,
-abstract = {A variety of processes have been identified as playing a key role in maintenance of hyper-rich tropical forest, among which ecological sorting caused by niche partitioning challenges stochastic dispersal processes. However, demographic responses to spatio-temporal resource variation that could result in biased species distributions are still little studied. In this paper we investigate from two censuses, c. 15 y apart, of a 12-ha permanent forest sample in French Guiana, how tree recruitment and mortality rates vary among hydrological soil types known to affect species habitat preferences and among ecological guilds related to species light requirement. The results indicate that both recruitment and mortality vary significantly with respect to these factors. While the mean instantaneous mortality and recruitment rates are estimated to 0.98 and 0.81{\%}, respectively, pioneer species, canopy trees and hydromorphic bottomland soils depart significantly from these values. In particular, the pioneers, regenerating either from the soil seed bank or from post-opening seed rain, show faster dynamics than other species. These two guilds harbour probabilities of mortality elevated by a factor of 1.9 and 3.2, respectively, and probabilities of recruitment elevated by a factor of 4.9 and 3.1, respectively. Conversely, canopy trees show slower dynamics, with probabilities of mortality and recruitment lowered by a mean factor of about 0.5 with respect to other species. We also observe that trees growing in hydromorphic bottomlands prove to have significantly higher mortality and recruitment probabilities, by a factor of about 2 with respect to those growing in terra firme.},
-annote = {Kcor},
-author = {Madelaine, C{\'{e}}cile and P{\'{e}}lissier, Rapha{\"{e}}l and Vincent, Greg and Molino, Jean-Fran{\c{c}}ois and Sabatier, Daniel and Pr{\'{e}}vost, Marie-Fran{\c{c}}oise and de Namur, C.},
-doi = {10.1017/S0266467406003944},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Madelaine et al. - 2007 - Mortality and recruitment in a lowland tropical rain forest of French Guiana effects of soil type and species.pdf:pdf},
-journal = {Journal of Tropical Ecology},
-number = {3},
-pages = {277},
-title = {{Mortality and recruitment in a lowland tropical rain forest of French Guiana: effects of soil type and species guild}},
-url = {http://www.journals.cambridge.org/abstract{\_}S0266467406003944},
-volume = {23},
-year = {2007}
-}
-@article{Haase1996,
-abstract = {Single species and bivariate distribution patterns in a semiarid shrubland in SE Spain, dominated by the tall leguminous shrub Retama sphaerocarpa, were investigated by second-order spatial analysis based on Ripley's K-function. Shrubs were significantly clumped because of a strong association of dwarf shrubs, mostly Artemisia barrelieri, under the canopy of R. sphaerocarpa. R. sphaerocarpa shrubs were randomly distributed, but when different size-classes were analysed separately, the pattern changed from significantly clumped to random and then to regular with increasing canopy diameter, suggesting increasing intraspecific competition with shrub size. A. barrelieri was significantly clumped at all scales because of aggregation under the canopy of large R. sphaerocarpa. The association between the species became stronger with increasing canopy diameter of R. sphaerocarpa, suggesting that facilitation prevailed over interspecific competition because of niche separation in different tiers, both above- and below ground. R. sphaerocarpa size thus determined both the type of pattern for its own size class and tier, and the scale and intensity of the association with its understorey shrubs.},
-author = {Haase, Peter and Pugnaire, Francisco I. and Clark, S. C. and Incoll, L. D.},
-doi = {10.2307/3236301},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Haase et al. - 1996 - Spatial patterns in a two-tiered semi-arid shrubland in southeastern Spain.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {527--534},
-title = {{Spatial patterns in a two-tiered semi-arid shrubland in southeastern Spain}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3236301/abstract;jsessionid=F71DEC274B03AA2D20A3EDCD4C0ACD62.f04t04},
-volume = {7},
-year = {1996}
-}
-@article{Escalas2013,
-abstract = {Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (), regional () and the overall difference between local communities (). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the , and components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (=+), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.},
-annote = {ISI Document Delivery No.: 230TY
-Times Cited: 0
-Cited Reference Count: 92
-Escalas, Arthur Bouvier, Thierry Mouchet, Maud A. Leprieur, Fabien Bouvier, Corinne Troussellier, Marc Mouillot, David
-EC2CO project FDFish [2008PRJ1]; ANR project BIODIVNEK
-This work was partially funded by an EC2CO project FDFish (2008PRJ1) and the ANR project BIODIVNEK. Authors would like to thank Alison Duncan for improving the English language of this manuscript, and two anonymous reviewers for insightful comments on this manuscript. The authors declare that they have no conflict of interest.
-Wiley-blackwell
-Hoboken},
-author = {Escalas, Arthur and Bouvier, Thierry and Mouchet, Maud A. and Leprieur, Fabien and Bouvier, Corinne and Troussellier, Marc and Mouillot, David},
-doi = {10.1111/1462-2920.12156},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Escalas et al. - 2013 - A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse sca.pdf:pdf},
-journal = {Environmental Microbiology},
-number = {10},
-pages = {2642--2657},
-title = {{A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales}},
-volume = {15},
-year = {2013}
-}
-@article{Legendre1993,
-abstract = {Autocorrelation is a very general statistical property of ecological variables observed across geographic space; its most common forms are patches and gradients. Spatial autocorrelation, which comes either from the physical forcing of environmental variables or from community processes, presents a problem for statistical testing because autocorrelated data violate the assumption of independence of most standard statistical procedures.The paper discusses first how autocorrelation in ecological variables can be described and measured, with emphasis on mapping techniques. Then, proper statistical testing in the presence of autocorrelation is briefly discussed. Finally, ways are presented of explicitly introducing spatial structures into ecological models. Two approaches are proposed; in the raw-data approach, the spatial structure takes the form of a polynomial of the x and y geographic coordinates of the sampling stations; in the matrix approach, the spatial structure is introduced in the form of a geographic distance matrix among locations. These two approaches are compared in the concluding section. A table provides a list of computer programs available for spatial analysis.},
-author = {Legendre, Pierre},
-doi = {10.2307/1939924},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre - 1993 - Spatial Autocorrelation Trouble or New Paradigm.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1659--1673},
-title = {{Spatial Autocorrelation: Trouble or New Paradigm?}},
-url = {http://www.jstor.org/stable/1939924},
-volume = {74},
-year = {1993}
-}
-@article{Head1996,
-abstract = {China's “Open Door” policy has created a natural experiment for studying agglomeration externalities and the role of incentives designed to attract foreign direct investment. We build a model which predicts that foreign firms will prefer cities where other foreign firms are located. We estimate the model using data on 931 foreign ventures. We then use simulations to explore the effect policies favoring particular cities had on the distribution of investment. We find that “attractive” cities—those with good infrastructure and an established industrial base—gained most and that agglomeration effects greatly magnified the direct impact of policy.},
-author = {Head, Keith and Ries, John},
-doi = {10.1006/juec.1996.0022},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Head, Ries - 1996 - Inter-City Competition for Foreign Investment Static and Dynamic Effects of China's Incentive Areas.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {1},
-pages = {38--60},
-title = {{Inter-City Competition for Foreign Investment: Static and Dynamic Effects of China's Incentive Areas}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119096900224},
-volume = {40},
-year = {1996}
-}
-@article{Wiegand2013,
-abstract = {Many functional summary characteristics such as Ripley's K function have been used in ecology to describe the spatial structure of point patterns to aid understanding of the underlying processes. However, their use is poorly guided in ecology because little is understood how well single summary characteristics, or a combination of them, capture the spatial structure of real world patterns. Here, we systematically tested the performance of combinations of eight summary characteristics [i.e. pair correlation function g(r), K-function K(r), the proportion E(r) of points with no neighbor at distance r, the nearest neighbor distribution function D(r), the spherical contact distribution Hs(r), the kth nearest-neighbor distribution functions Dk(r), the mean distance nn(k) to the kth neighbor, and the intensity function $\lambda$(x)]. To this end we used point pattern data covering a wide range of spatial structures including simulated (stationary) as well as real, possibly non-stationary, patterns on tree species in a tropical forest in Panam{\'{a}}. To measure the information contained in a given combination of summary characteristics we used simulated annealing to reconstruct the observed patterns based only on the limited information provided by this combination and assessed how well other characteristics of the observed pattern were recovered. We found that the number of summary characteristics required to capture the spatial structure of stationary patterns varied between one (for patterns with near random structures) and three (for patterns with complex cluster and superposition structures), but with a robust ranking g(r), Dk(r), and Hs(r) that was largely independent on pattern idiosyncrasies. Stationary summary characteristics [with ranking g(r), Dk(r), Hs(r), E(r)] captured small- to intermediate scale properties of non-stationary patterns, but for describing large-scale spatial structures the intensity function was required. Our finding revealed that the current practice in ecology of using only one or two summary characteristics bears danger that essential characteristics of more complex patterns would not be detected. The technique of pattern reconstruction presented here has wide applications in ecology.},
-author = {Wiegand, Thorsten and He, Fangliang and Hubbell, Stephen P.},
-doi = {10.1111/j.1600-0587.2012.07361.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wiegand, He, Hubbell - 2013 - A systematic comparison of summary characteristics for quantifying point patterns in ecology.pdf:pdf},
-journal = {Ecography},
-number = {1},
-pages = {92--103},
-title = {{A systematic comparison of summary characteristics for quantifying point patterns in ecology}},
-url = {http://dx.doi.org/10.1111/j.1600-0587.2012.07361.x},
-volume = {36},
-year = {2013}
-}
-@article{Johnson1996,
-abstract = {Attempts to unveil the relationships between the taxonomic diversity, productivity and stability of ecosystems continue to generate inconclusive, contradictory and controversial conclusions. New insights from recent studies support the hypothesis that species diversity enhances productivity and stability in some ecosystems, but not in others. Appreciation is growing for the ways that particular ecosystem features, such as environmental variability and nutrient stress, can influence biotic interactions. Alternatives to the diversity-stability hypothesis have been proposed, and experimental approaches are starting to evolve to test these hypotheses and to elucidate the mechanisms underlying the functional role of species diversity.},
-author = {Johnson, Kris H. and Vogt, Kristiina A. and Clark, Heidi J. and Schmitz, Oswald J. and Vogt, Daniel J.},
-doi = {10.1016/0169-5347(96)10040-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Johnson et al. - 1996 - Biodiversity and the productivity and stability of ecosystems.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {9},
-pages = {372--377},
-title = {{Biodiversity and the productivity and stability of ecosystems.}},
-url = {http://www.sciencedirect.com/science/article/pii/0169534796100409},
-volume = {11},
-year = {1996}
-}
-@article{Zacharias2001,
-abstract = {1. Focal species (i.e. indicators, keystones, umbrellas, and flagships) have been advocated for the management and conservation of natural environments. 2. The assumption has been that the presence or abundance of a focal species is a means to understanding the composition and/or state of the more complex community. 3. We review the characteristics of focal species, and evaluate their appropriateness and utility judged against conservation objectives. 4. It appears that indicator species (of both composition and condition) may be of greatest general utility, and that several types of focal species may exhibit useful indicator properties.},
-author = {Zacharias, Mark A. and Roff, John C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zacharias, Roff - 2001 - Use of focal species in marine conservation and management a review and critique.pdf:pdf},
-journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
-number = {1},
-pages = {59--76},
-title = {{Use of focal species in marine conservation and management: a review and critique}},
-url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.429/abstract},
-volume = {11},
-year = {2001}
-}
-@article{Grassberger1988,
-abstract = {We derive the systematic corrections to estimates of generalized (Renyi) entropies and to generalized dimensions Dq from finite data sets. As an application, we discuss correlation estimates of Dq for the H{\'{e}}non map. We end with some remarks about lacunarity measures.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Grassberger, Peter},
-doi = {10.1016/0375-9601(88)90193-4},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grassberger - 1988 - Finite sample corrections to entropy and dimension estimates.pdf:pdf},
-journal = {Physics Letters A},
-number = {6-7},
-pages = {369--373},
-title = {{Finite sample corrections to entropy and dimension estimates}},
-url = {http://www.sciencedirect.com/science/article/pii/0375960188901934},
-volume = {128},
-year = {1988}
-}
-@article{Guerin2015,
-abstract = {Applications are needed to map biodiversity from large-scale species occurrence datasets whilst seamlessly integrating with existing functions in R. Phylogenetic endemism (PE) is a biodiversity measure based on range-restricted phylogenetic diversity (PD). Current implementations use area of occupancy (AOO) or frequency to estimate the spatial range of branch-length (i.e. phylogenetic range-rarity), rather than extent of occurrence (EOO; i.e. georeferenced phylogenetic endemism), which is known to produce different range estimates. We present R functions to map PD or PE weighted by AOO or EOO (new georeferenced implementation), taking as inputs georeferenced species occurrences and a phylogeny. Non-parametric statistics distinguish PD/PE from trivial correlates of species richness and sampling intensity.},
-author = {Guerin, Greg R. and Lowe, Andrew J.},
-doi = {10.1016/j.softx.2015.10.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Guerin, Lowe - 2015 - Mapping phylogenetic endemism in R using georeferenced branch extents.pdf:pdf},
-journal = {SoftwareX},
-pages = {22--26},
-title = {{Mapping phylogenetic endemism in R using georeferenced branch extents}},
-url = {http://dx.doi.org/10.1016/j.softx.2015.10.002},
-volume = {3-4},
-year = {2015}
-}
-@misc{Wing2004,
-abstract = {Unnamed fossil fruits and leaves from the macroflora from the Cerraj{\'{o}}n Formation, Guaj{\'{i}}ra Peninsula, northeastern Colombia},
-author = {Wing, S L and Herrera, F and Jaramillo, C A},
-booktitle = {VII International Organization of Paleobotany Conference Abstracts.},
-pages = {146--147},
-title = {{Paleocene flora from the Cerraj{\'{o}}n Formation, Guaj{\'{i}}ra Peninsula, northeastern Colombia}},
-year = {2004}
-}
-@article{Moeur1993,
-abstract = {Procedures for stem-mapping trees on fixed area plots are described. Two statistical procedures for analyzing spatial patterns of the completely mapped tree data are presented. These procedures, known as nearest neighbor analysis and Ripley's K(d) function, consider the cumulative distributions of distances between trees, compared to a distance distribution for a point pattern generated by a random process. Nearest neighbor uses tree-to-nearest-tree distances, and Ripley's K(d) considers distances between all pairs of trees. Both procedures include edge correction schemes for trees near plot boundaries. The two analyses were applied to stem-mapped data from several old-growth study plots to investigate spatial interactions within and between groups of canopy trees. Patterns for trees in different mortality, size, and competitive classes were analyzed separately. Results showed that between-tree competitive interactions drive forest patterns from clustering toward regularity. There was also evidence that canopy gaps are an important mechanism in the regeneration process. The examples illustrate how spatial pattern analysis can be useful in describing and interpreting complicated development processes that result from competitive interactions between individual trees.},
-author = {Moeur, Melinda},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moeur - 1997 - Spatial models of competition and gap dynamics in old-growth Tsuga heterophylla Thuja plicata forests.pdf:pdf},
-journal = {Forest Science},
-number = {4},
-pages = {756--775},
-title = {{Characterizing spatial patterns of trees using stem-mapped data}},
-url = {http://www.ingentaconnect.com/content/saf/fs/1993/00000039/00000004/art00012},
-volume = {39},
-year = {1993}
-}
-@article{Martins1997,
-abstract = {This article considers the statistical issues relevant to the comparative method in evolutionary biology. A generalized linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character. Our approach thus emphasizes the similarity among evolutionary questions asked in comparative studies. We then discuss ways of specifying the sources of error involved in a comparative study (e.g., measurement error, error due to evolution along a phylogeny, error due to misspecification of a phylogeny) and show how the impact of these sources of error can be taken into account in a comparative analysis. In contrast to most existing phylogenetic comparative methods, our procedure offers substantial flexibility in the choice of microevolutionary assumptions underlying the statistical analysis, allowing researchers to choose assumptions that are most appropriate for their particular set of data and evolutionary question. In developing the approach, we also propose novel ways of incorporating within- species variation and / or measurement error into phylogenetic analyses, of estimating ancestral states, and of considering both continuous (quantitative) and categorical (qualitative or "state") characters in the same analysis.},
-author = {Martins, Em{\'{i}}lia P. and Hansen, Thomas F.},
-doi = {10.1086/286013},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Martins, Hansen - 1997 - Phylogenies and the Comparative Method A General Approach to Incorporating Phylogenetic Information into the An.pdf:pdf},
-journal = {The American Naturalist},
-number = {4},
-pages = {646},
-title = {{Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data}},
-url = {http://www.journals.uchicago.edu/doi/abs/10.1086/286013},
-volume = {149},
-year = {1997}
-}
-@article{Blanchet2011,
-abstract = {During the last 20 years, ecologists discovered the importance of including spatial relationships in models of species distributions. Among the latest developments in modelling how species are spatially structured are eigenfunction-based spatial filtering methods such as Moran's eigenvector maps (MEM) and principal coordinates of neighbour matrices (PCNM). Although these methods are very powerful and flexible, they are only suited to study distributions resulting from non-directional spatial processes. The asymmetric eigenvector map (AEM) framework, a new eigenfunction-based spatial filtering method, fills this theoretical gap. AEM was specifically designed to model spatial structures hypothesized to be produced by directional spatial processes. Water currents, prevailing wind on mountainsides, river networks, and glaciations at historical time scales are some of the situations where AEM can be used. This paper presents three applications of the method illustrating different combinations of: sampling schemes (regular and irregular), data types (univariate and multivariate), and spatial scales (metres, kilometres, and hundreds of kilometres). The applications include the distribution of a crustacean (Atya) in a river, bacterial production in a lake, and the distribution of the copepodite stages of a crustacean on the Atlantic oceanic shelf. In each application, a comparison is made between AEM, MEM, and PCNM. No environmental components were included in the comparisons. AEM was a strong predictor in all cases, explaining 59.8{\%} for Atya distribution, 51.4{\%} of the bacterial production variation, and 38.4{\%} for the copepodite distributions. AEM outperformed MEM and PCNM in these applications, offering a powerful and more appropriate tool for spatial modelling of species distributions under directional forcing and leading to a better understanding of the processes at work in these systems.},
-author = {Blanchet, F. Guillaume and Legendre, Pierre and Maranger, Roxane and Monti, Dominique and Pepin, Pierre},
-doi = {10.1007/s00442-010-1867-y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Blanchet et al. - 2011 - Modelling the effect of directional spatial ecological processes at different scales.pdf:pdf},
-journal = {Oecologia},
-number = {2},
-pages = {357--368},
-title = {{Modelling the effect of directional spatial ecological processes at different scales}},
-url = {http://link.springer.com/article/10.1007/s00442-010-1867-y},
-volume = {166},
-year = {2011}
-}
-@article{Zhang2015,
-abstract = {Alpha, beta, and gamma diversity are three fundamental biodiversity components in ecology, but most studies focus only on the scale issues of the alpha or gamma diversity component. The beta diversity component, which incorporates both alpha and gamma diversity components, is ideal for studying scale issues of diversity. We explore the scale dependency of beta diversity and scale relationship, both theoretically as well as by application to actual data sets. Our results showed that a power law exists for beta diversity-area (spatial grain or spatial extent) relationships, and that the parameters of the power law are dependent on the grain and extent for which the data are defined. Coarse grain size generates a steeper slope (scaling exponent z) with lower values of intercept (c), while a larger extent results in a reverse trend in both parameters. We also found that, for a given grain (with varying extent) or a given extent (with varying grain) the two parameters are themselves related by power laws. These findings are important because they are the first to simultaneously relate the various components of scale and di- versity in a unified manner. Abbreviations:},
-author = {Zhang, Y. and Ma, K. and Anand, Madhur and Ye, W. and Fu, B.},
-doi = {10.1556/168.2015.16.1.5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Zhang et al. - 2015 - Scale dependence of the beta diversity-scale relationship.pdf:pdf},
-journal = {Community Ecology},
-number = {1},
-pages = {39--47},
-title = {{Scale dependence of the beta diversity-scale relationship}},
-url = {http://www.akademiai.com/doi/abs/10.1556/168.2015.16.1.5},
-volume = {16},
-year = {2015}
-}
-@article{Belevitch1959,
-abstract = {The rank-frequency diagrams of statistical linguistics are reinterpreted as distribution curves of the cumulative probability of types in the ccttaloguc versus the probability of tokens in the text. For such distributions, the closure condition "Sum of p =1" (which does not hold in general statistics for the independent variables) imposes certain relations between the mean, the variance, the number of elements in the catalogue and the average information content (negative entropy). Sections 2 to 4 are devoted to the mathematics of these reations, especially to their particular forms for truncated normal distributions. First and second order Taylor approximations to an arbitrary distribution law take the form of Zipf's and Mandelbrot's laws respectively. Experimented data lead to accept the truncated normal distribution with sigma close to 2.8 bits as the general law for words. Data on letter and phoneme distributions seem to indicate that the standard deviation has the universal value sigma close to 1.4 bits.},
-author = {Belevitch, V.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Belevitch - 1959 - On the statistical laws of linguistic distributions.pdf:pdf},
-journal = {Annales de la Soci{\'{e}}t{\'{e}} Scientifique de Bruxelles},
-number = {3},
-pages = {310--326},
-title = {{On the statistical laws of linguistic distributions}},
-url = {http://www.csl.sri.com/users/neumann/belevitch.pdf},
-volume = {73},
-year = {1959}
-}
-@article{Feser2000,
-abstract = {This paper uses input-output data combined with point process modeling techniques to test whether enterprises linked within nominal buyer-supplier chains have a greater propensity to cluster in space than manufacturing enterprises in general. The methodology controls for the general tendency of firms to seek locations in concentrated agglomerations and isolates lates the influence of firm interdependence on spatial clustering. Our findings suggest that there is indeed an association between economic linkages and geographic clustering in our study area, but only for some types of economic clusters, mainly those that are comprised mainly of more knowledge-based or technology-intensive sectors. In general, we endeavor to show that spatial analytical methods hold considerable promise for conducting rigorous tests of industrial location questions.},
-author = {Feser, Edward J. and Sweeney, Stuart H.},
-doi = {10.1007/PL00011462},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser, Sweeney - 2000 - A test for the coincident economic and spatial clustering of business enterprises.pdf:pdf},
-journal = {Journal of Geographical Systems},
-number = {4},
-pages = {349--373},
-title = {{A test for the coincident economic and spatial clustering of business enterprises}},
-url = {http://link.springer.com/article/10.1007/PL00011462},
-volume = {2},
-year = {2000}
-}
-@article{Cadotte2010a,
-abstract = {Aim: In an era of global habitat loss and species extinction, conservation biology is increasingly becoming a science of triage. A key approach has been the designation of global biodiversity hotspots - areas of high species richness and endemism - prioritizing regions that are disproportionately valuable. However, traditional hotspot approaches leave absent information on species evolutionary histories. We argue that prioritizing the preservation of evolutionary diversity is one way to maximize genotypic and functional diversity, providing ecosystems with the greatest number of options for dealing with an uncertain future. Location: Global. Methods: We review methods for encapsulating phylogenetic diversity and distinctiveness and provide an illustration of how phylogenetic metrics can be extended to include data on geographical rarity and inform conservation prioritization at biogeographic scales. Results: Abundance-weighted metrics of evolutionary diversity can be used to simultaneously prioritize populations, species, habitats and biogeographical regions. Main conclusion: Policy makers need to know where scarce conservation funds should be focused to maximize gains and minimize the loss of biological diversity. By incorporating these evolutionary diversity metrics into prioritization schemes, managers can better quantify the valuation of different regions based on evolutionary information.},
-author = {Cadotte, Marc W. and {Jonathan Davies}, T.},
-doi = {10.1111/j.1472-4642.2010.00650.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cadotte, Jonathan Davies - 2010 - Rarest of the rare Advances in combining evolutionary distinctiveness and scarcity to inform conservat.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {3},
-pages = {376--385},
-title = {{Rarest of the rare: Advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales}},
-volume = {16},
-year = {2010}
-}
-@incollection{Vellend2010,
-address = {Oxford},
-author = {Vellend, Mark and Cornwell, William K. and Magnuson-Ford, Karen and Mooers, Arne {\O}.},
-booktitle = {Biological diversity: frontiers in measurement and assessment},
-editor = {Magurran, Anne E and McGill, Brian J},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Vellend et al. - 2010 - Measuring phylogenetic biodiversity.pdf:pdf},
-pages = {194--207},
-publisher = {Oxford University Press},
-title = {{Measuring phylogenetic biodiversity}},
-url = {http://phylodiversity.net/wcornwell/Vellend{\_}etal{\_}2011{\_}bookchap.pdf},
-year = {2010}
-}
-@article{Hardy2008,
-abstract = {1. To characterize the spatial phylogenetic structure of communities, Hardy {\&} Senterre (2007) (J. Ecol., 95, 493-506) partition Gini-Simpson diversity and its generalization, Rao's entropy, defining I-ST and P-ST as the proportion of diversity expressed among sites. 2. Interpreting I-ST as a measure of 'differentiation' between sites is inadequate because low values are actually compatible with high differentiation (low species sharing) in species rich communities. To avoid an inadequate use of I-ST, for example in conservation biology, we offer a more literal interpretation: I-ST expresses the 'local species identity excess'. Similarly, P-ST expresses the 'local phylogenetic similarity excess'. 3. Villeger {\&} Mouillot (2008) (J. Ecol., 96, 845-848, this issue) argue that the equations of Hardy {\&} Senterre (2007) to compute diversity are inadequate when sites differ in size, and they provide new expressions weighting sites by their sizes. We argue that whether sites must be weighted equally or not depends on the question being asked. Moreover, actual size and sample size must be distinguished, the latter being important for defining estimators. 4. Synthesis. The formulations given by Hardy {\&} Senterre (2007) and by Villeger {\&} Mouillot (2008)are both correct in the specific contexts we detail.},
-annote = {Times Cited: 9},
-author = {Hardy, Olivier J. and Jost, Lou},
-doi = {10.1111/j.1365-2745.2008.01423.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hardy, Jost - 2008 - Interpreting and estimating measures of community phylogenetic structuring.pdf:pdf},
-journal = {Journal of Ecology},
-number = {5},
-pages = {849--852},
-title = {{Interpreting and estimating measures of community phylogenetic structuring}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2008.01423.x/abstract},
-volume = {96},
-year = {2008}
-}
-@article{Graham2008,
-abstract = {A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.},
-author = {Graham, Catherine H. and Fine, Paul V. A.},
-doi = {10.1111/j.1461-0248.2008.01256.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Graham, Fine - 2008 - Phylogenetic beta diversity linking ecological and evolutionary processes across space in time.pdf:pdf},
-journal = {Ecology Letters},
-number = {12},
-pages = {1265--1277},
-title = {{Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time}},
-url = {http://dx.doi.org/10.1111/j.1461-0248.2008.01256.x},
-volume = {11},
-year = {2008}
-}
-@article{Mulder2002,
-abstract = {Positive relationships between species richness and ecosystem processes such as productivity or nitrogen cycling can be the result of a number of mechanisms. We examined how species richness, biomass, and legume presence, diversity, and abundance explained nitrogen dynamics in experimental grassland plots in northern Sweden. Nitrogen concentrations and $\delta$15N values were measured in plants grown in 28 mixtures (58 plots) including 1, 2, 4, 8 or 12 local grassland species over four years. Values for $\delta$15N declined over time for all three functional groups (grasses, legumes, and non-leguminous forbs), suggesting greater reliance on N fixed by legumes over time by all species. Above ground percent nitrogen ({\%}N) also declined over time but root {\%}N and total N did not. Path analysis of above ground data suggested that two main factors affected {\%}N and the size of the N pool. First, higher plant diversity (species richness) increased total N through increased biomass in the plot. Although in the first two years of the experiment this was the result of a greater probability of inclusion of at least one legume, in the last two years diversity had a significant effect on biomass beyond this effect. Second, percent legumes planted in the plots had a strong effect on above ground {\%}N and $\delta$15N, but a much smaller effect on above ground biomass. In contrast, greater plant diversity affected N in roots both by increasing biomass and by decreasing {\%}N (after controlling for effects mediated by root biomass and legume biomass). Increased legume biomass resulted in higher {\%}N and lower $\delta$15N for both non-legume forbs and grasses in the first year, but only for grasses in the third year. We conclude that a sampling effect (greater probability of including a legume) contributed towards greater biomass and total N in high-diversity communities early on in the experiment, but that over time this effect weakened and other positive effects of diversity became more important.},
-author = {Mulder, C. P. H. and Jumpponen, A. and H{\"{o}}gberg, P. and Huss-Danell, K.},
-doi = {10.1007/s00442-002-1043-0},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Mulder et al. - 2002 - How plant diversity and legumes affect nitrogen dynamics in experimental grassland communities.pdf:pdf},
-journal = {Oecologia},
-number = {3},
-pages = {412--421},
-title = {{How plant diversity and legumes affect nitrogen dynamics in experimental grassland communities}},
-url = {http://link.springer.com/article/10.1007/s00442-002-1043-0},
-volume = {133},
-year = {2002}
-}
-@article{Sterner1986,
-abstract = {(1) Spatial patterns of the mortality of tropical trees were investigated using maps of four species on an 80 x 80-m site of primary rainforest in Costa Rica. Using new statistical methodology, designed specifically for complete maps of individuals, models of clustering or uniformity were fitted to different size classes, and the relative uniformity of the different size classes compared. The data for the extant juveniles were then used to predict what the extant adult spatial distribution would be given random mortality of the juveniles. The actual adult distribution was compared to this hypothetical distribution to see if they were more or less uniform than predicted. (2) For three of the four species, the spatial models which fit the adults were more uniform than the models which fit the juveniles. The adults of these three species were significantly more uniformly distributed than expected from the random mortality of their extant juveniles. The fourth species had adults with a similar distribution to randomly thinned extant juveniles. (3) Post-germination survival leads toward a uniform distribution. During the lifespan of three of the four species, repulsion occurs between individuals. At small scales, clumping, when present, may be more the result of patchy dispersal of seeds or seedling germination than the patchy survival of germinated individuals.},
-author = {Sterner, Robert W. and Ribic, Christine A. and Schatz, George E.},
-doi = {10.2307/2260386},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sterner, Ribic, Schatz - 1986 - Testing for Life Historical Changes in Spatial Patterns of Four Tropical Tree Species.pdf:pdf},
-journal = {Journal of Ecology},
-number = {3},
-pages = {621--633},
-title = {{Testing for Life Historical Changes in Spatial Patterns of Four Tropical Tree Species}},
-url = {http://www.jstor.org/stable/2260386},
-volume = {74},
-year = {1986}
-}
-@article{Lamosova2010,
-abstract = {Plant species create aggregations of conspecifics as a consequence of limited seed dispersal, clonal growth and heterogeneous environment. Such intraspecific aggregation increases the importance of intraspecific competition relative to interspecific competition which may slow down competitive exclusion and promote species coexistence. To examine howspatial aggregation impacts the functioning of experimental assemblages of varying species richness, eight perennial grassland species of different growth form were grown in random and aggregated patterns in monocultures, two-, four-, and eight-species mixtures. In mixtures with an aggregated pattern, monospecific clumps were interspecifically segregated. Mixed model ANOVA was used to test (i) how the total productivity and productivity of individual species is affected by the number of species in a mixture, and (ii) how these relationships are affected by spatial pattern of sown plants. The main patterns of productivity response to species richness conform to other studies: non-transgressive overyielding is omnipresent (the productivity of mixtures is higher than the average of its constituent species so that the net diversity, selection and complementarity effects are positive), whereas transgressive overyielding is found only in a minority of cases (average of log(over- yielding) being close to zero or negative). The theoretical prediction that plants in a random pattern should produce more than in an aggregated pattern (the distances to neighbours are smaller and consequently the competition among neighbours stronger) was confirmed in monocultures of all the eight species. The situation is more complicated in mixtures, probably as a consequence of complicated interplay between interspecific and intraspecific competition. The most productive species (Achillea, Holcus, Plantago) were competitively superior and increased their relative productivity with mixture richness. The intraspecific competition of these species is stronger than that of most other species. The aggregated pattern in the full mixture increased the survival of subordinate species, and consequently, we conclude that an aggregated pattern can promote species coexistence (or at least postpone competitive exclusion), particularly in comparison with homogeneously sown mixtures. ?},
-author = {Lamo{\v{s}}ov{\'{a}}, Tereza and Dole{\v{z}}al, Jiř{\'{i}} and Lanta, Vojt{\v{e}}ch and Lep{\v{s}}, Jan},
-doi = {10.1016/j.actao.2010.02.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lamo{\v{s}}ov{\'{a}} et al. - 2010 - Spatial pattern affects diversity–productivity relationships in experimental meadow communities.pdf:pdf},
-journal = {Acta Oecologica},
-number = {3},
-pages = {325--332},
-title = {{Spatial pattern affects diversity-productivity relationships in experimental meadow communities}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1146609X10000160},
-volume = {36},
-year = {2010}
-}
-@article{Chao2012a,
-abstract = {There have been intense debates about the decomposition of regional diversity (gamma) into its within-community component (alpha) and between-community component (beta). Although a recent Ecology Forum achieved consensus in the use of ‘‘numbers equivalents'' (Hill numbers) as the proper choice of diversity measure, three related major issues were still left unresolved. (1) What is the precise meaning of the ‘‘independence'' or ‘‘statistical independence'' of alpha diversity and beta diversity? (2) Which partitioning (additive vs. multiplicative) should be used for a given application? (3) What is the proper formula for alpha diversity, as there are two formulas in the literature? This paper proposes a possible resolution to each of these issues. For the first issue, we clarify the definitions of ‘‘independence'' and ‘‘statistical independence'' from two perspectives so that confusion about this issue can be cleared up. We also discuss the causes of dependence, so that the dependence relationship between any two diversity components in both partitioning schemes can be rigorously justified by theory and also intuitively understood by simulation. For the second issue, both multiplicative and additive beta diversities based on Hill numbers are useful measures and quantify different aspects of communities. However, neither can be directly applied to compare relative compositional similarity or differentiation across multiple regions with different numbers of communities because multiplicative beta diversity depends on the number of communities, and additive beta diversity additionally depends on alpha (equivalently, on gamma). Such dependences should be removed. We propose transformations to remove these dependences, and we show that the transformed multiplicative beta and additive beta both lead to the same classes of measures, which are always in a range of [0, 1] and thus can be used to compare relative similarity or differentiation among communities across multiple regions. These similarity measures include multiple-community generalizations of the S{\o}renson, Jaccard, Horn, and Morisita-Horn measures. For the third issue, we present some observations including a finding about which alpha formula produces independent alpha and beta components. These may help to resolve the choice of a proper formula for alpha diversity. Some related issues are also briefly discussed.},
-author = {Chao, Anne and Chiu, Chun-Huo and Hsieh, T. C.},
-doi = {10.1890/11-1817.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu, Hsieh - 2012 - Proposing a resolution to debates on diversity partitioning(2).pdf:pdf},
-journal = {Ecology},
-number = {9},
-pages = {2037--2051},
-title = {{Proposing a resolution to debates on diversity partitioning}},
-url = {http://dx.doi.org/10.1890/11-1817.1},
-volume = {93},
-year = {2012}
-}
-@article{Lookingbill2000,
-abstract = {European Mediterranean landscapes have undergone changes in structure in recent years as a result of widespread agricultural land abandonment and cessation of silvicultural regimes. Studies concerning the regeneration dynamics of dominant forest species have become critical to the prediction of future landscape trends in these changing forest stands. Quercus ilex (holm oak) and Q. pubescens (downy oak) are considered to be the terminal point of secondary succession in extensive areas of the Mediterranean region. Recent studies, however, have suggested the existence of recruitment bottlenecks in oak genet populations as a result of current management regimes. In this study, we present evidence of the successful establishment of Q. ilex and Q. pubescens in Pinus halepensis (Aleppo pine) woodlands. We investigate the distribution patterns and spatial relationships among oak recruits and resident pines. Established P. halepensis is randomly distributed throughout the study area. Oak seedlings are positively associated with pine trees, suggesting that P. halepensis individuals provide safe sites for oak genet recruitment. We show that spatial patterns of recruitment are in agreement with the general model of spatial segregation described for other Mediterranean plant communities, with seeder species colonizing large openings after disturbance, followed by a more aggregated recruitment of resprouter species.},
-annote = {Article
-English
-J VEG SCI
-365GA},
-author = {Lookingbill, T. R. and Zavala, M. A.},
-doi = {10.2307/3246590},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lookingbill, Zavala - 2000 - Spatial pattern of Quercus ilex and Quercus pubescens recruitment in Pinus halepensis dominated woodlands.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {607--612},
-title = {{Spatial pattern of Quercus ilex and Quercus pubescens recruitment in Pinus halepensis dominated woodlands}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/3246590/abstract},
-volume = {11},
-year = {2000}
-}
-@article{Shimatani2001a,
-abstract = {When pairwise differences (relatedness) between species are numerically given, the average of the species differences weighted by relative frequencies can be used as a species diversity index. This paper first theoretically develops the indices of this type, then applies them to forestry data. As examples of diversity indices, this paper explores the taxonomic diversity and the newly introduced amino acid diversity, which is a modification of the nucleotide diversity in genetics. The first, mathematical part shows that both indices can be decomposed into three inner factors; evenness of relative frequencies (=the Simpson index), the simple average over species differences regardless of relative frequencies, and the taxonomic or genetic balance in relative frequencies. The taxonomic diversity has another decomposition: the sum over the Simpson indices at all the taxonomic levels. The second part examines the effects of different forest management techniques on diversity. It is shown that a thinning operation for promoting survival of specific desirable species also contributed to increasing the taxonomic diversity. If we calculated only conventional indices that do not incorporate species relatedness, we would simply conclude that the thinning did not significantly affect the diversity. The theoretical developments of the first part complement the result, leading us to a better interpretation about contrasting vegetation structures. The mathematical results also reveal that the amino acid diversity involves redundant species, which is undesirable when measuring diversity; hence, this index is used to demonstrates crucial points when we introduce species relatedness. The results suggest further possibilities of applying diversity indices incorporating species differences to a variety of ecological studies.},
-author = {Shimatani, Kenichiro},
-doi = {10.1034/j.1600-0706.2001.930115.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shimatani - 2001 - On the measurement of species diversity incorporating species differences.pdf:pdf},
-journal = {Oikos},
-number = {1},
-pages = {135--147},
-title = {{On the measurement of species diversity incorporating species differences}},
-url = {http://dx.doi.org/10.1034/j.1600-0706.2001.930115.x},
-volume = {93},
-year = {2001}
-}
-@article{Triantis2012,
-abstract = {Aim We conducted the most extensive quantitative analysis yet undertaken of the form taken by the island species–area relationship (ISAR), among 20 models, to determine: (1) the best-fit model, (2) the best-fit model family, (3) the best-fit ISAR shape (and presence of an asymptote), (4) system properties that may explain ISAR form, and (5) parameter values and interpretation of the logarithmic implementation of the power model. Location World-wide. Methods We amassed 601 data sets from terrestrial islands and employed an information-theoretic framework to test for the best-fit ISAR model, family, and shape, and for the presence/absence of an asymptote. Two main criteria were applied: generality (the proportion of cases for which the model provided an adequate fit) and efficiency (the overall probability of a model, when adequate, being the best at explaining ISARs; evaluated using the mean overall AICc weight). Multivariate analyses were used to explore the potential of island system properties to explain trends in ISAR form, and to describe variation in the parameters of the logarithmic power model. Results Adequate fits were obtained for 465 data sets. The simpler models performed best, with the power model ranked first. Similar results were obtained at model family level. The ISAR form is most commonly convex upwards, without an asymptote. Island system traits had low descriptive power in relation to variation in ISAR form. However, the z and c parameters of the logarithmic power model show significant pattern in relation to island system type and taxon. Main conclusions Over most scales of space, ISARs are best represented by the power model and other simple models. More complex, sigmoid models may be applicable when the spatial range exceeds three orders of magnitude. With respect to the log power model, z-values are indicative of the process(es) establishing species richness and composition patterns, while c-values are indicative of the realized carrying capacity of the system per unit area. Variation in ISAR form is biologically meaningful, but the signal is noisy, as multiple processes constrain the ecological space available within island systems and the relative importance of these processes varies with the spatial scale of the system.},
-author = {Triantis, Kostas A. and Guilhaumon, Fran{\c{c}}ois and Whittaker, Robert J.},
-doi = {10.1111/j.1365-2699.2011.02652.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Triantis, Guilhaumon, Whittaker - 2012 - The island species–area relationship biology and statistics.pdf:pdf},
-journal = {Journal of Biogeography},
-number = {2},
-pages = {215--231},
-title = {{The island species–area relationship: biology and statistics}},
-url = {http://dx.doi.org/10.1111/j.1365-2699.2011.02652.x},
-volume = {39},
-year = {2012}
-}
-@article{Aldrich2003,
-abstract = {An analysis of spatial dispersion was conducted for individual tree species in the old-growth forest at the Davis-Purdue Research Forest in Indiana. This 20.6 ha stand has been left largely undisturbed by exogenous factors since its acquisition by Purdue in 1917. It is the only long-term study plot of its size for a temperate hardwood forest with x-y coordinates (rectangular plot) for all species above 10 cm diameter. Full censuses have been conducted spanning 60 years (1926, 1976 and 1986). Ripley's L(t) function revealed that most species are characterized by some form of aggregation, agreeing with a prior evaluation from 1981. Heterogeneity of spatial structure was evident between two large plots, indicating that differences in site quality and history had influenced spatial structure. Shade-intolerant species were numerically dominant and spatially aggregated in 1926 but have declined over the 60-year interval and become more random in spatial dispersion. Shade-tolerant species have increased in number and become more aggregated over time, or they exhibit little change in spatial structure. Examples of the latter include Acer saccharum and Ulmus americana, species that experienced explosive population growth. These contrasting patterns are masked by stand-level patterns that show a trend toward uniformity over the same time frame. These data reveal that changes in dispersion accompany the demographic failure experienced by numerous tree species in Central Hardwood old-growth stands, and these changes may feed back into a negative population cycle and further impede regeneration. The simultaneous manipulation of dispersion and density should be considered as a tool for influencing forest succession and promoting regeneration of desired tree species. Published by Elsevier B.V.},
-annote = {Article
-English
-FOREST ECOL MANAGE
-703YX},
-author = {Aldrich, P. R. and Parker, George R. and Ward, Jeffrey S. and Michler, C. H.},
-doi = {10.1016/S0378-1127(02)00612-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Aldrich et al. - 2003 - Spatial dispersion of trees in an old-growth temperate hardwood forest over 60 years of succession.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {475--491},
-title = {{Spatial dispersion of trees in an old-growth temperate hardwood forest over 60 years of succession}},
-volume = {180},
-year = {2003}
-}
-@article{Pavoine2009a,
-abstract = {Phylogenetic divergences have recently been included in analyses that aim to elucidate patterns of biodiversity in space and time. We introduce a generalized framework for two widely used phylogenetic diversity (PD) indices: Rao's quadratic entropy (QE) and Faith's PD. We demonstrate how this framework can be used to partition diversity simultaneously across evolutionary periods and spatial (e.g. local communities in a region) and/or time units (e.g. a community investigated yearly). From a study of rockfish hotspot diversity from the Southern California Bight, the analysis of PD revealed a recent decrease in the amount of fish caught from six evolutionary deep lineages, with implications for the community structure of this speciose group. This approach, which can also be applied to trees assembled from functional traits, contributes to our understanding of the mechanisms that underpin community organization and to the description of the consequences of human-driven impacts in the environment. {\^{A}}{\textcopyright} 2009 Blackwell Publishing Ltd/CNRS.},
-annote = {Cited By (since 1996): 11
-Export Date: 30 December 2011
-Source: Scopus
-CODEN: ECLEF
-doi: 10.1111/j.1461-0248.2009.01344.x
-PubMed ID: 19601954
-Language of Original Document: English
-Correspondence Address: Pavoine, S.; Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom; email: pavoine@mnhn.fr},
-author = {Pavoine, Sandrine and Love, Milton S. and Bonsall, Michael B.},
-doi = {10.1111/j.1461-0248.2009.01344.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pavoine, Love, Bonsall - 2009 - Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogeneticall.pdf:pdf},
-journal = {Ecology Letters},
-number = {9},
-pages = {898--908},
-title = {{Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages: Application to rockfish (genus: Sebastes) in the Southern California Bight}},
-url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-68849130477{\&}partnerID=40{\&}md5=587aa7251fdb620c02ddaef2c396cdb6},
-volume = {12},
-year = {2009}
-}
-@article{Marcon2013,
-abstract = {Ripley's K function is the classical tool to characterize the spatial structure of point patterns. It is widely used in vegetation studies. Testing its values against a null hypothesis usually relies on Monte-Carlo simulations since little is known about its distribution. We introduce a statistical test against complete spatial randomness (CSR). The test returns the p-value to reject the null hypothesis of independence between point locations. It is more rigorous and faster than classical Monte-Carlo simulations. We show how to apply it to a tropical forest plot. The necessary R code is provided.},
-author = {Marcon, Eric and Traissac, St{\'{e}}phane and Lang, Gabriel},
-doi = {10.1155/2013/753475},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Traissac, Lang - 2013 - A Statistical Test for Ripley's Function Rejection of Poisson Null Hypothesis.pdf:pdf},
-journal = {ISRN Ecology},
-number = {Article ID 753475},
-pages = {9},
-title = {{A Statistical Test for Ripley's Function Rejection of Poisson Null Hypothesis}},
-url = {http://www.hindawi.com/journals/isrn/2013/753475/abs/},
-volume = {2013},
-year = {2013}
-}
-@article{Chao2016a,
-abstract = {There are many concepts and measures of beta diversity and related similarity/differentiation indices. The variance framework (derived from the total variance of a community species abundance matrix) and diversity decomposition (based on partitioning gamma diversity into alpha and beta components) are two major approaches. There have been no bridges/links between the two approaches. Here, we establish a bridge by extending and modifying each approach so that both lead to the same classes of similarity/differentiation measures, which range in the interval [0, 1] and which can be compared across multiple sets of communities. Our extension/modification in each approach is based on the following major differences between the two approaches. (i) In the decomposition approach, a diversity order q that controls sensitivity to species abundances is used, whereas there is no such order involved in the variance approach. (ii) Transformations of raw abundances are typically used in the variance approach, whereas abundances are not transformed in diversity decomposition. (iii) The variance-based beta for non-transformed data is implicitly related to (and constrained by) alpha, gamma and total abundance. Namely, the attained maximum value of this beta when communities are completely distinct (no shared species) is not a fixed constant; the maximum varies with alpha, gamma and total abundance. By contrast, the beta component obtained from the multiplicative decomposition is not constrained by alpha, gamma and total abundance. To construct the bridge, we extend the variance of community data to a class of divergence measures (parameterized by an order q) and use normalization to remove these measures' constraints by alpha, gamma and total abundance. The resulting normalized divergence measures are legitimate differentiation measures. In the decomposition approach, we adopt a modified multiplicative decomposition scheme; the resulting beta component can be transformed to quantify compositional similarity/differentiation among communities. Then, the similarity/differentiation measures obtained from the extended variance framework turn out to be identical to those from the modified diversity decomposition, establishing the bridge. Other types of similarity/differentiation measures (e.g. N-community Bray–Curtis type) and extension to phylogenetic and functional versions are discussed. A real example using corals is given for illustration.},
-author = {Chao, Anne and Chiu, Chun-huo},
-doi = {10.1111/2041-210X.12551},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu - 2016 - Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation(3).pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {8},
-pages = {919--928},
-title = {{Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12551/abstract},
-volume = {7},
-year = {2016}
-}
-@book{Husch2016,
-author = {Kershaw, John A. Jr. and Ducey, Mark J. and Beers, Thomas W. and Husch, Bertram},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kershaw et al. - 2017 - Forest mensuration.pdf:pdf},
-isbn = {9781118902004},
-publisher = {Wiley-Blackwell},
-title = {{Forest mensuration}},
-year = {2017}
-}
-@article{Wennekes2012,
-abstract = {Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species' differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species' differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.},
-author = {Wennekes, Paul L and Rosindell, James and Etienne, Rampal S},
-doi = {10.1007/s10441-012-9144-6},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wennekes, Rosindell, Etienne - 2012 - The neutral-niche debate a philosophical perspective.pdf:pdf},
-journal = {Acta biotheoretica},
-number = {3},
-pages = {257--71},
-title = {{The neutral-niche debate: a philosophical perspective.}},
-url = {http://dx.doi.org/10.1007/s10441-012-9144-6},
-volume = {60},
-year = {2012}
-}
-@article{Wilsey2005,
-abstract = {Although many indices estimate diversity, species richness recently has been used as a surrogate for diversity in many studies in ecology, biogeography, and conservation. Underlying assumptions of this approach are that all diversity indices, including those that weight species importance by their relative abundance (e.g., evenness), are correlated positively, and that richness accounts for a large proportion of the variance in diversity. We addressed these assumptions with data from six grassland sites using univariate and multivariate analyses of a variety of indices (species evenness, richness, rarity, dominance, and Simpson's diversity index). Univariate correlations between plant species evenness and richness were weak and negative at each site. Principal-component analyses consistently revealed two significant components of variation in diversity. Richness and evenness were largely orthogonal, with Simpson's diversity loading between them. Thus, measures of species diversity based on relative abundance, as well as richness, may be necessary to capture the full complexity of diversity in conservation studies and in experiments of biodiversity and ecosystem functioning. At these and perhaps other sites, species richness was an incomplete surrogate for diversity.},
-author = {Wilsey, Brian J. and Chalcraft, David R. and Bowles, Christy M. and Willig, Michael R.},
-doi = {10.1890/04-0394},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wilsey et al. - 2005 - Relationships among indicies suggest that richness is an imcomplete surrogate for grassland diversity.pdf:pdf},
-isbn = {0012-9658},
-journal = {Ecology},
-number = {5},
-pages = {1178--1184},
-title = {{Relationships among indicies suggest that richness is an imcomplete surrogate for grassland diversity}},
-volume = {86},
-year = {2005}
-}
-@article{Schulte2005,
-abstract = {Fisher's alpha is a satisfactory scale-independent indicator of biodiversity. However, alpha may be underestimated in communities in which the spatial arrangement of individuals is strongly clustered, or in which the total number of species does not tend to infinity. We have extended Fisher's curve to allow for an accurate calibration of Fisher's alpha in such communities. In spite of its good performance, the use of this extended curve is complicated by its optimization procedure. Therefore, we have simulated the extended Fisher curve by modifying the smooth expolinear curve, using three ecologically meaningful parameters only, i.e. Fisher's alpha, a coefficient describing the effects of clustering and the maximum number of species. The resulting equations successfully describe species-individual relationships from both spatial and temporal observations on both plant and animal communities. This family of equations combines three advantages: Fisher's alpha can be quantified more accurately, the number of estimated parameters is flexible and can be kept to a minimum, while all parameters can legitimately be compared across sites.},
-author = {Schulte, Rogier P. O. and Lantinga, Egbert A. and Hawkins, Michael J.},
-doi = {10.1016/j.jtbi.2004.08.014},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Schulte, Lantinga, Hawkins - 2005 - A new family of Fisher-curves estimates Fisher's alpha more accurately.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {3},
-pages = {305--313},
-title = {{A new family of Fisher-curves estimates Fisher's alpha more accurately}},
-url = {http://www.sciencedirect.com/science/article/B6WMD-4DD8GDH-2/1/33df5b59271c61b520d1d326a5e6df3c},
-volume = {232},
-year = {2005}
-}
-@article{Rutledge1976,
-abstract = {Ecological stability defined as the ability of an ecosystem to resist changes in the presence of perturbations leads to consideration of the effective choice of the pathways for energy flow. The roles of diversity and complexity (i.e. interdependence) in determining stability arise naturally in the development of an index from the qualitative concepts of information theory. As a tool for ecosystem analysis, the stability measure developed in this paper is applied to two example systems.},
-author = {Rutledge, Robert W. and Basore, Benett L. and Mulholland, Robert J.},
-doi = {10.1016/0022-5193(76)90007-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rutledge, Basore, Mulholland - 1976 - Ecological stability an information theory viewpoint.pdf:pdf},
-journal = {Journal of theoretical biology},
-number = {2},
-pages = {355--371},
-title = {{Ecological stability: an information theory viewpoint.}},
-volume = {57},
-year = {1976}
-}
-@article{Enquist2015,
-abstract = {Aim: More powerful tests of biodiversity theories need to move beyond species richness and explicitly focus on mechanisms generating diversity via trait composition. The rise of trait-based ecology has led to an increased focus on the distribution and dynamics of traits across broad geographic and climatic gradients and how these distributions influence ecosystem function. However, a general theory of trait-based ecology, that can apply across different scales (e.g. species that differ in size) and gradients (e.g. temperature), has yet to be formulated. While research focused on metabolic and allometric scaling theory provides the basis for such a theory, it does not explicitly account for differences in traits within and across taxa, such as variation in the optimal temperature for growth. Here we synthesize trait-based and metabolic scaling approaches into a framework that we term 'Trait Driver Theory' or TDT. It shows that the shape and dynamics of trait and size distributions can be linked to fundamental drivers of community assembly and how the community will respond to future drivers. To assess predictions and assumptions of TDT, we review several theoretical studies and recent empirical studies spanning local and biogeographic gradients. Further, we analyze how the shift in trait distributions influences ecosystem processes across an elevational gradient and a 140-year-long ecological experiment. We show that TDT provides a baseline for (i) recasting the predictions of ecological theories based on species richness in terms of the shape of trait distributions and (ii) integrating how specific traits, including body size, and functional diversity then 'scale up' to influence ecosystem functioning and the dynamics of species assemblages across climate gradients. Further, TDT offers a novel framework to integrate trait, metabolic/allometric, and species-richness-based approaches to better predict functional biogeography and how assemblages of species have and may respond to climate change.},
-author = {Enquist, Brian J. and Norberg, Jon and Bonser, Stephen P. and Violle, Cyrille and Webb, Colleen T. and Henderson, Amanda and Sloat, Lindsey L. and Savage, Van M.},
-doi = {10.1016/bs.aecr.2015.02.001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Enquist et al. - 2015 - Scaling from Traits to Ecosystems Developing a General Trait Driver Theory via Integrating Trait-Based and Metab.pdf:pdf},
-journal = {Advances in Ecological Research},
-pages = {249--318},
-title = {{Scaling from Traits to Ecosystems: Developing a General Trait Driver Theory via Integrating Trait-Based and Metabolic Scaling Theories}},
-url = {http://www.sciencedirect.com/science/article/pii/S0065250415000070},
-volume = {52},
-year = {2015}
-}
-@book{Pellens2016,
-author = {Pellens, Roseli and Grandcolas, Philippe},
-doi = {10.1007/978-3-319-22461-9},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pellens, Grandcolas - 2016 - Biodiversity Conservation and Phylogenetic Systematics.pdf:pdf},
-isbn = {978-3-319-22460-2},
-publisher = {Springer Open},
-title = {{Biodiversity Conservation and Phylogenetic Systematics}},
-url = {http://link.springer.com/10.1007/978-3-319-22461-9},
-volume = {14},
-year = {2016}
-}
-@article{Beck2010,
-abstract = {1. Measuring biodiversity quantitatively is a key component to its investigation, but many methods are known to be biased by undersampling (i.e. incomplete inventories), a common situation in ecological field studies. 2. Following a long tradition of comparing measures of alpha diversity to judge their usefulness, we used simulated data to assess bias of nine diversity measures – some of them proposed fairly recently, such as estimating true species richness depending on the completeness of inventories (Brose, U. {\&} Martinez, N.D. Oikos (2004) 105, 292), bias-corrected Shannon diversity (Chao, A. {\&} Shen, T.-J. Environmental and Ecological Statistics (2003) 10, 429), while others are commonly applied (e.g. Shannon's entropy, Fisher's $\alpha$) or long known but rarely used (estimating Shannon's entropy from Fisher's $\alpha$). 3. We conclude that the ‘effective number of species' based on bias-corrected Shannon's entropy is an unbiased estimator of diversity at sample completeness c. {\textgreater}0{\textperiodcentered}5, while below that it is still less biased than, e.g., estimated species richness (Brose, U. {\&} Martinez, N.D. Oikos (2004) 105, 292). 4. Fisher's $\alpha$ cannot be tested with the same rigour because it cannot measure the diversity of completely inventoried communities, and we present simulations illustrating this effect when sample completeness approaches high values. However, we can show that Fisher's $\alpha$ produces relatively stable values at low sample completeness (an effect previously shown only in empirical data), and we tentatively conclude that it may still be considered a good (possibly superior) measure of diversity if completeness is very low.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Beck, Jan and Schwanghart, Wolfgang},
-doi = {10.1111/j.2041-210X.2009.00003.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beck, Schwanghart - 2010 - Comparing measures of species diversity from incomplete inventories an update.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {1},
-pages = {38--44},
-title = {{Comparing measures of species diversity from incomplete inventories: an update}},
-url = {http://dx.doi.org/10.1111/j.2041-210X.2009.00003.x},
-volume = {1},
-year = {2010}
-}
-@article{Pachepsky2001,
-abstract = {The study of patterns in living diversity is driven by the desire to find the universal rules that underlie the organization of ecosystems. The relative abundance distribution, which characterizes the total number and abundance of species in a community, is arguably the most fundamental measure in ecology. Considerable effort has been expended in striving for a general theory that can explain the form of the distribution. Despite this, a mechanistic understanding of the form in terms of physiological and environmental parameters remains elusive. Recently, it has been proposed that space plays a central role in generating the patterns of diversity. Here we show that an understanding of the observed form of the relative abundance distribution requires a consideration of how individuals pack in time. We present a framework for studying the dynamics of communities which generalizes the prevailing species-based approach to one based on individuals that are characterized by their physiological traits. The observed form of the abundance distribution and its dependence on richness and disturbance are reproduced, and can be understood in terms of the trade-off between time to reproduction and fecundity.},
-author = {Pachepsky, Elizaveta and Crawford, John W. and Bown, James L. and Squire, Geoff},
-doi = {10.1038/35073563},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Pachepsky et al. - 2001 - Towards a general theory of biodiversity.pdf:pdf},
-isbn = {0028-0836},
-issn = {0028-0836},
-journal = {Nature},
-number = {6831},
-pages = {923--926},
-pmid = {11309615},
-title = {{Towards a general theory of biodiversity.}},
-volume = {410},
-year = {2001}
-}
-@article{Jangid2016,
-abstract = {K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina{\textregistered} libraries generated from US homes, K-shuff required {\textgreater}300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina{\textregistered} libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.},
-author = {Jangid, Kamlesh and Kao, Ming-Hung and Lahamge, Aishwarya and Williams, Mark A. and Rathbun, Stephen L. and Whitman, William B.},
-doi = {10.1371/journal.pone.0167634},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jangid et al. - 2016 - K-shuff A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.pdf:pdf},
-journal = {Plos One},
-number = {12},
-pages = {e0167634},
-title = {{K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries}},
-url = {http://dx.plos.org/10.1371/journal.pone.0167634},
-volume = {11},
-year = {2016}
-}
-@book{Gillespie2016,
-author = {Gillespie, Colin and Lovelace, Robin},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gillespie, Lovelace - 2016 - Efficient R Programming.pdf:pdf},
-isbn = {1491950781},
-pages = {150},
-publisher = {O'Reilly Media},
-title = {{Efficient R Programming}},
-url = {https://csgillespie.github.io/efficientR/},
-year = {2016}
-}
-@article{Legendre1999,
-abstract = {We present a new multivariate technique for testing the significance of in- dividual terms in a multifactorial analysis-of-variance model for multispecies response variables. The technique will allow researchers to base analyses on measures of association (distance measures) that are ecologically relevant. In addition, unlike other distance-based hypothesis-testing techniques, this method allows tests of significance of interaction terms in a linear model. The technique uses the existing method of redundancy analysis (RDA) but allows the analysis to be based on Bray-Curtis or other ecologically meaningful measures through the use of principal coordinate analysis (PCoA). Steps in the procedure include: (1) calculating a matrix of distances among replicates using a distance measure of choice (e.g., Bray-Curtis); (2) determining the principal coordinates (including a correction for negative eigenvalues, if necessary), which preserve these distances; (3) creating a matrix of dummy variables corresponding to the design of the experiment (i.e., individual terms in a linear model); (4) analyzing the relationship between the principal coordinates (species data) and the dummy variables (model) using RDA; and (5) implementing a test by permutation for particular statistics corresponding to the particular terms in the model. This method has certain advantages not shared by other multivariate testing procedures. We demonstrate the use of this technique with experimental ecological data from intertidal assemblages and show how the presence of significant multivariate interactions can be interpreted. It is our view that distance-based RDA will be extremely useful to ecologists measuring multispecies responses to structured multifactorial experimental designs.},
-author = {Legendre, Pierre and Anderson, Marti J.},
-doi = {10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Legendre, Anderson - 1999 - Distance-based redundancy analysis testing multispecies responses in multifactorial ecological experiments.pdf:pdf},
-journal = {Ecological Monographs},
-number = {1},
-pages = {1--24},
-title = {{Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments}},
-url = {http://www.esajournals.org/doi/abs/10.1890/0012-9615(1999)069{\%}5B0001:DBRATM{\%}5D2.0.CO;2},
-volume = {69},
-year = {1999}
-}
-@article{Shepard2002,
-abstract = {The spatial relationships exhibited by individuals in a population may indicate their social organization. In territorial species interactions between individuals should lead to maximal spacing in a uniform pattern. Using nearest neighbor distances (NND), I tested for territoriality in the green frog (Rana clamitans) by determining if males were uniformly dispersed within breeding choruses. Observed dispersion patterns were not consistent with territoriality. Males were randomly dispersed on all seven nights during the breeding period, four of five nights during the nonbreeding period and uniformly dispersed on one night during the nonbreeding period. Dispersion did not differ between periods although density was higher and NND was smaller during the breeding period. There was also no correlation between male size and NND. The disparity of my results might be explained by differences in male density and resource distribution and its effect on habitat quality since these factors influence behavior and spacing. Alternatively, uniform spacing may not be a reliable characteristic of territoriality.},
-author = {Shepard, Donald B.},
-doi = {10.1674/0003-0031(2002)148[0394:SROMGF]2.0.CO;2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shepard - 2002 - Spatial Relationships of Male Green Frogs (Rana clamitans) throughout the Activity Season.pdf:pdf},
-journal = {The American Midland Naturalist},
-number = {2},
-pages = {394--400},
-title = {{Spatial Relationships of Male Green Frogs (Rana clamitans) throughout the Activity Season}},
-url = {http://www.bioone.org/doi/abs/10.1674/0003-0031(2002)148{\%}5B0394{\%}3ASROMGF{\%}5D2.0.CO{\%}3B2},
-volume = {148},
-year = {2002}
-}
-@article{Leps2006,
-abstract = {Quantifying the functional diversity in ecological communities is very promising for both studying the response of diversity to environmental gradients and the effects of diversity on ecosystem functioning (i.e. in “biodiversity experiments”). In our view, the Rao coefficient is a good candidate for an efficient functional diversity index. It is, in fact, a generalization of the Simpson's index of diversity and it can be used with various measures of dissimilarity between species (both those based on a single trait and those based on several traits). However, when intending to quantify the functional diversity, we have to make various methodological decisions such as how many and which traits to use, how to weight them, how to combine traits that are measured at different scales and how to quantify the species' relative abundances in a community. Here we discuss these issues with examples from real plant communities and argue that diversity within a single trait is often the most ecologically relevant information. When using indices based on many traits, we plead for careful a priori selection of ecologically relevant traits, although other options are also feasible.When combining many traits, often with different scales, methods considering the extent of species overlap in trait space can be applied for both the qualitative and quantitative traits. Another possibility proposed here is to decompose the variability of a trait in a community according to the relative effect of among- and within-species differentiation (with the latter not considered by current indices of functional diversity), in a way analogical to decomposition of Sum of squares in ANOVA. Further, we showwhy the functional diversity is more tightly related to species diversity (measured by Simpson index) when biomass is used as a measure of population abundance, in comparison with frequency. Finally, the general expectation is that functional diversity can be a better predictor of ecosystem functioning than the number of species or the number of functional groups. However, we demonstrate that some of the expectations might be overrated – in particular, the “sampling effect” in biodiversity experiments is not avoided when functional diversity is used as a predictor.},
-author = {Lep{\v{s}}, Jan and {De Bello}, Francesco and Lavorel, Sandra and Berman, Sandra},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lep{\v{s}} et al. - 2006 - Quantifying and interpreting functional diversity of natural communities practical considerations matter.pdf:pdf},
-journal = {Preslia},
-pages = {481--501},
-title = {{Quantifying and interpreting functional diversity of natural communities: practical considerations matter}},
-url = {http://hal.archives-ouvertes.fr/halsde-00293183/},
-volume = {78},
-year = {2006}
-}
-@book{Clausius1868,
-address = {Paris},
-author = {Clausius, Rudolf},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Th{\'{e}}orie{\_}m{\'{e}}canique{\_}de{\_}la{\_}chaleur.pdf:pdf},
-publisher = {Eug{\`{e}}ne Lacroix},
-title = {{Th{\'{e}}orie m{\'{e}}canique de la chaleur}},
-year = {1868}
-}
-@article{Ostling2003,
-abstract = {Power-law relationships appear to characterize many patterns observed in ecology, from the level of individuals to the level of ecosystems (Calder 1984, Gaston and Blackburn 2000). These power laws often hold over scale ranges sufficiently large to justify the search for a unifying theoretical framework explaining the relationship between these patterns. A promising avenue for discovering such a framework is the exploration of the fractal properties from which these power laws derive and their implications for other ecological characteristics. In this vein, Harte and Kinzig (1997) and Harte et al. (1999a) studied the fractal property behind a power-law species-area relationship and its implications for other species distribution characteristics. In a recent paper published in Oikos, Lennon et al. (2002) claim that in order to derive a power-law species-area relationship from fractals in the distribution of species, Harte et al. (1999a) assumed that individual species distributions are fractal and that all species patterns have the same fractal dimension D. Inspired by empirical evidence that indicates that fractal dimension tends to vary between species, they then show that in this more realistic case of varying D, the species-area relationship does not follow a power law. Hence Lennon et al. (2002) conclude that, despite Harte et al. (1999a) derivation of the power-law species-area relationship from fractals, a fractal distribution of species is not what produces power-law species-area relationships in nature. We show here the misleading error in Lennon et al.'s (2002) critique. Harte et al. (1999a) did not derive the power-law species-area relationship from fractals at the ‘species-level', but rather from a ‘community-level' fractal property that can hold without the presence of ‘species-level' fractals. Furthermore, this community-level fractal property holds in any region where the power-law species-area relationship holds (Harte and Kinzig 1997). Hence this community-level fractal property must be what produces power-law species-area relationships in nature – it is equivalent to it. Lennon et al. are correct that if the species-level fractal property holds for each species in a community, a power-law species-area relationship will result only if the fractal dimension is constant across species. This result was found previously in Harte et al. (2001), where the overall degree of compatibility between the community-level and species-level fractal properties was derived. However, as Harte et al. (2001) showed, the community-level fractal property and hence the power-law species-area relationship can exist either if the fractal dimension is constant across species, or if some individual species distributions are not fractal on their own. This does not rule out the possibility that species-level fractals are important in nature. Below we provide a detailed analysis of these issues.},
-author = {Ostling, Annette and Harte, John and Green, Jessica L. and Kinzig, Ann P.},
-doi = {10.1034/j.1600-0706.2003.12600.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ostling et al. - 2003 - A community-level fractal property produces power-law species-area relationships.pdf:pdf},
-isbn = {1600-0706},
-issn = {0030-1299},
-journal = {Oikos},
-number = {1},
-pages = {218--224},
-title = {{A community-level fractal property produces power-law species-area relationships}},
-url = {http://dx.doi.org/10.1034/j.1600-0706.2003.12600.x},
-volume = {103},
-year = {2003}
-}
-@article{Hill2001,
-abstract = {Two classifications are presented that organize the major processes and theories addressing the high species diversity of tropical rain forests. The first typology organizes environmental and biological processes within a spatio-temporal hierarchy, whilst the second classifies 12 theories according to over-arching driving forces: genetic differentiation, environ- mental change, niche/habitat diversification and biotic interaction. The theories are reviewed and evaluated by delineating the development and current state of academic knowledge pertaining to each. General issues that arise from examining species diversity within the tropical realm are discussed and this indicates where the academic debate stands today. Some thoughts concerning future research avenues are included.},
-author = {Hill, J. L. and Hill, R. A.},
-doi = {10.1177/030913330102500302},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hill, Hill - 2001 - Why are tropical rain forests so species rich Classifying, reviewing and evaluating theories.pdf:pdf},
-isbn = {0309-1333},
-issn = {0309-1333},
-journal = {Progress in Physical Geography},
-number = {3},
-pages = {326--354},
-pmid = {10183},
-title = {{Why are tropical rain forests so species rich? Classifying, reviewing and evaluating theories}},
-url = {http://journals.sagepub.com/doi/10.1177/030913330102500302},
-volume = {25},
-year = {2001}
-}
-@article{Wolda1981,
-abstract = {The effect of sample size and species diversity on a variety of similarity indices is explored. Real values of a similarity index must be evaluated relative to the expected maximum value of that index, which is the value obtained for samples randomly drawn from the same universe, with the diversity and sample sizes of the real samples. It is shown that these expected maxima differ from the theoretical maxima, the values obtained for two identical samples, and that the relationship between expected and theoretical maxima depends on sample size and on species diversity in all cases, without exception, In all cases but one (the Morisita index) the expected maxima depend strongly to fairly strongly on sample size and diversity. For some of the more useful indices empirical equations are given to calculate the expected maxi- mum value of the indices to which the observed values can be related at any combination of sample sizes. It is recom- mended that the Morisita index be used whenever possible to avoid the complex dealings with effects of sample size and diversity; however, when previous logarithmic transformation of the data is required, which often may be the case, the Morisita-Horn or the Renkonen indices are recommended.},
-author = {Wolda, Henk},
-doi = {10.1007/BF00344966},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wolda - 1981 - Similarity indices, sample size and diversity.pdf:pdf},
-journal = {Oecologia},
-number = {3},
-pages = {296--302},
-title = {{Similarity indices, sample size and diversity}},
-url = {http://link.springer.com/10.1007/BF00344966},
-volume = {50},
-year = {1981}
-}
-@article{Colwell1994,
-abstract = {Both the magnitude and the urgency of the task of assessing global biodiversity require that we make the most of what we know through the use of estimation and extrapolation. Likewise, future biodiversity inventories need to be designed around the use of effective sampling and estimation procedures, especially for `hyperdiverse' groups of terrestrial organisms, such as arthropods, nematodes, fungi, and microorganisms. The challenge of estimating patterns of species richness from samples can be separated into (i) the problem of estimating local species richness, and (ii) the problem of estimating the distinctness, or complementarity, of species assemblages. These concepts apply on a wide range of spatial, temporal, and functional scales. Local richness can be estimated by extrapolating species accumulation curves, fitting parametric distributions of relative abundance, or using non-parametric techniques based on the distribution of individuals among species or of species among samples. We present several of these methods and examine their effectiveness for an example data set. We present a simple measure of complementarity, with some biogeographic examples, and outline the difficult problem of estimating complementarity from samples. Finally, we discuss the importance of using `reference' sites (or sub-sites) to assess the true richness and composition of species assemblages, to measure ecologically significant ratios between unrelated taxa, to measure taxon/sub-taxon (hier-archical) ratios, and to `calibrate' standardized sampling methods. This information can then be applied to the rapid, approximate assessment of species richness and faunal or floral composition at `comparative' sites.},
-author = {Colwell, Robert K. and Coddington, Jonathan A.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Colwell, Coddington - 1994 - Estimating Terrestrial Biodiversity through Extrapolation.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1311},
-pages = {101--118},
-title = {{Estimating Terrestrial Biodiversity through Extrapolation}},
-url = {http://www.jstor.org/stable/56143},
-volume = {345},
-year = {1994}
-}
-@article{Arbia2009a,
-abstract = {In this paper we propose a new class of spatial concentration measures to verify hypotheses on the spatial concentration of empirical phenomena. Our proposed measures incorporate the ideas of both a-spatial concentration and spatial autocorrelation. We discuss many issues related to the approximate sampling theory and we suggest a Monte Carlo test for the presence of significant spatial concentration. A simulation experiment studying the relationship of the new measure to different spatial patterns and to different levels of a-spatial variability is also reported. A discussion related to irregular space is included. (C) 2009 Elsevier B.V. All rights reserved.},
-annote = {ISI Document Delivery No.: 504NV
-Times Cited: 0
-Cited Reference Count: 49
-Arbia, Giuseppe Piras, Gianfranco
-ELSEVIER SCIENCE BV},
-author = {Arbia, Giuseppe and Piras, G.},
-doi = {10.1016/j.csda.2009.07.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arbia, Piras - 2009 - A new class of spatial concentration measures.pdf:pdf},
-journal = {Computational Statistics {\&} Data Analysis},
-number = {12},
-pages = {4471--4481},
-title = {{A new class of spatial concentration measures}},
-volume = {53},
-year = {2009}
-}
-@article{DeLong1996,
-author = {DeLong, Don C. Jr},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/DeLong - 1996 - Defining Biodiversity.pdf:pdf},
-journal = {Wildlife Society Bulletin},
-number = {4},
-pages = {738--749},
-title = {{Defining Biodiversity}},
-url = {http://www.jstor.org/stable/3783168},
-volume = {24},
-year = {1996}
-}
-@article{Alonso-Villar2013,
-abstract = {The goal of this paper is to offer an analytical framework within which relative concentration, including both the concentration of each sector and aggregate concentration, can be analysed. By borrowing properties from the literature on income inequality and segregation and adapting them to a location context, this paper characterizes the generalized entropy family of concentration indexes and shows the properties of the L-index. In addition, it offers other measures taken from the segregation literature. All these tools are used to analyse the spatial patterns of manufacturing industries in Spain from 1977 to 2008, paying special attention to their technological intensity.},
-annote = {Si},
-author = {Alonso-Villar, Olga and {Del R{\'{i}}o}, Coral},
-doi = {10.1080/00343404.2011.587796},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Alonso-Villar, Del Rio - 2013 - Concentration of Economic Activity An Analytical Framework.pdf:pdf},
-journal = {Regional Studies},
-number = {5},
-pages = {756--772},
-title = {{Concentration of Economic Activity: An Analytical Framework}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/00343404.2011.587796},
-volume = {47},
-year = {2013}
-}
-@book{Gourlet-Fleury2004,
-address = {Paris},
-author = {Gourlet-Fleury, Sylvie and Guehl, Jean Marc and Laroussinie, OIivier},
-publisher = {Elsevier},
-title = {{Ecology {\&} management of a neotropical rainforest. Lessons drawn from Paracou, a long-term experimental research site in French Guiana}},
-year = {2004}
-}
-@article{Havrda1967,
-author = {Havrda, Jan and Charv{\'{a}}t, Franti{\v{s}}ek},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Havrda, Charv{\'{a}}t - 1967 - Quantification method of classification processes. Concept of structural alpha-entropy.pdf:pdf},
-journal = {Kybernetika},
-number = {1},
-pages = {30--35},
-title = {{Quantification method of classification processes. Concept of structural alpha-entropy}},
-url = {https://eudml.org/doc/28681},
-volume = {3},
-year = {1967}
-}
-@article{Jensen2011,
-abstract = {Measuring the spatial distribution of locations of many entities (trees, atoms, economic activities, etc.), and, more precisely, the deviations from purely random configurations, is a powerful method to unravel their underlying interactions. Several coefficients have been developed in the past to quantify the possible deviations. It is important to quantify the variances of the coefficients for random distributions, to ascertain the statistical significance of an empirical deviation. By lack of a proper analytical expression, the significance is usually obtained by simulating many random configurations by Monte Carlo simulations. In the present paper, we present an exact analytical expression for the variance of several spatial coefficients for random distributions, and we rigorously show that these distributions asymptotically follow a Normal law. These two results eliminate the need for cumbersome Monte Carlo simulations. They also allowto understand qualitatively the main factors that may change the variance: number of sites, spatial inhomogeneity, etc.},
-author = {Jensen, Pablo and Michel, Julien},
-doi = {10.1007/s00168-009-0342-3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jensen, Michel - 2011 - Measuring spatial dispersion exact results on the variance of random spatial distributions.pdf:pdf},
-journal = {The Annals of Regional Science},
-number = {1},
-pages = {81--110},
-title = {{Measuring spatial dispersion: exact results on the variance of random spatial distributions}},
-url = {http://dx.doi.org/10.1007/s00168-009-0342-3},
-volume = {47},
-year = {2011}
-}
-@article{Nekola2002,
-abstract = {The occurrence of ten butterfly taxa (Clossiana eunomia dawsonii, Clossiana freija, Clossiana frigga, Clossiana titania, Coenonympha inornata, Erebia discoidalis, Incisalia augustinus, Lycaena dorcas, Lycaena epixanthe and Oeneis jutta) was analysed within three acid peatland habitat types from the Lake Superior drainage basin of northwestern Wisconsin, USA. Both first-(nearest-neighbour spatial analysis) and second-order (Ripley's K) spatial point process statistics were used to identify the extents over which each distribution pattern significantly deviated from random expectations. Versions of these tests were used that identified significant spatial pattern uncorrelated to habitat location and habitat preference. These analyses documented non-random occurrence patterns in seven species. Deviations from random were largely confined to two extents: {\textless}50 km and 70-100+ km. The majority of non-random patterns at {\textless}50 km extents were examples of aggregation, while the majority of non-random patterns noted at the 70-100+ km scale were examples of segregation. These results demonstrate that even for winged animals inside a limited landscape, spatially constrained processes can be important determinants of distribution. It is likely that metapopulation dynamics and dispersal limitation help explain why aggregation is dominant at small scales. The mechanisms underlying the predominance of segregation at large scales are less clear, but may be related to migration history and/or weak environmental gradients.},
-author = {Nekola, Jeffrey C. and Kraft, Clifford E.},
-doi = {10.1007/s004420100782},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Nekola, Kraft - 2002 - Spatial constraint of peatland butterfly occurrences within a heterogeneous landscape.pdf:pdf},
-journal = {Oecologia},
-number = {1},
-pages = {53--61},
-title = {{Spatial constraint of peatland butterfly occurrences within a heterogeneous landscape}},
-url = {http://link.springer.com/article/10.1007/s004420100782},
-volume = {130},
-year = {2002}
-}
-@article{Poisot2012,
-abstract = {1. Ecological specialization is a unifying concept in the biological sciences. While there are reliable ways to characterize specificity at individual and community levels, the evaluation of population and species-level measures is lacking. There is a need for such assessments given that populations and species are the relevant scales formost ecological and evolutionary processes. 2. Using examples of simulated and empirical data sets of bipartite networks representing a contin- uum of biological interactions, we evaluate six indices of specificity in terms of their robustness to incomplete sampling and information they extract fromdata. 3. Robustness differed between the measures and in their ability to differentiate specialists and generalists along a full continuum. On the empirical data sets, indices were less separated by their informativity than on the simulated data sets, whichmay be due to the heterogeneity of the former. 4. Based on these different evaluations for species-level (or population-level) specificity, we recom- mend the use of Resource range when no quantitative data are available and Paired Difference Index otherwise. These results will assist both applied and fundamental researchers in the character- ization and interpretation of species specificity},
-author = {Poisot, Timoth{\'{e}}e and Canard, Elsa and Mouquet, Nicolas and Hochberg, Michael E.},
-doi = {10.1111/j.2041-210X.2011.00174.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Poisot et al. - 2012 - A comparative study of ecological specialization estimators.pdf:pdf},
-journal = {Methods in Ecology and Evolution},
-number = {3},
-pages = {537--544},
-title = {{A comparative study of ecological specialization estimators}},
-url = {http://doi.wiley.com/10.1111/j.2041-210X.2011.00174.x},
-volume = {3},
-year = {2012}
-}
-@article{Jizhong1991,
-abstract = {An information entropy index is presented to measure ecosystem diversity based on the numbers of components and the strengths of interactions between them.},
-author = {Jizhong, Zhou and Shijun, Ma and Changming, Chen},
-doi = {10.1016/0304-3800(91)90176-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jizhong, Shijun, Changming - 1991 - An index of ecosystem diversity.pdf:pdf},
-journal = {Ecological Modelling},
-pages = {151--163},
-title = {{An index of ecosystem diversity}},
-url = {http://www.sciencedirect.com/science/article/pii/0304380091901762},
-volume = {59},
-year = {1991}
-}
-@article{Gibson2011,
-abstract = {Human-driven land-use changes increasingly threaten biodiversity, particularly in tropical forests where both species diversity and human pressures on natural environments are high(1). The rapid conversion of tropical forests for agriculture, timber production and other uses has generated vast, human-dominated landscapes with potentially dire consequences for tropical biodiversity(2-5). Today, few truly undisturbed tropical forests exist, whereas those degraded by repeated logging and fires, as well as secondary and plantation forests, are rapidly expanding(6,7). Here we provide a global assessment of the impact of disturbance and land conversion on biodiversity in tropical forests using a meta-analysis of 138 studies. We analysed 2,220 pairwise comparisons of biodiversity values in primary forests (with little or no human disturbance) and disturbed forests. We found that biodiversity values were substantially lower in degraded forests, but that this varied considerably by geographic region, taxonomic group, ecological metric and disturbance type. Even after partly accounting for confounding colonization and succession effects due to the composition of surrounding habitats, isolation and time since disturbance, we find that most forms of forest degradation have an overwhelmingly detrimental effect on tropical biodiversity. Our results clearly indicate that when it comes to maintaining tropical biodiversity, there is no substitute for primary forests.},
-author = {Gibson, Luke and Lee, Tien Ming and Koh, Lian Pin and Brook, Barry W. and Gardner, Toby A. and Barlow, Jos and Peres, Carlos a. and Bradshaw, Corey J. A. and Laurance, William F. and Lovejoy, Thomas E. and Sodhi, Navjot S.},
-doi = {10.1038/nature10425},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gibson et al. - 2011 - Primary forests are irreplaceable for sustaining tropical biodiversity.pdf:pdf},
-journal = {Nature},
-number = {7369},
-pages = {378--381},
-title = {{Primary forests are irreplaceable for sustaining tropical biodiversity}},
-url = {http://dx.doi.org/10.1038/nature10425},
-volume = {478},
-year = {2011}
-}
-@article{Baddeley2000,
-abstract = {We develop methods for analysing the 'interaction' or dependence between points in a spatial point pattern, when the pattern is spatially inhomogeneous. Completely non-parametric study of interactions is possible using an analogue of the K-function. Alternatively one may assume a semi-parametric model in which a (parametrically specified) homogeneous Markov point process is subjected to (non-parametric) inhomogeneous independent thinning. The effectiveness of these approaches is tested on datasets representing the positions of trees in forests.},
-author = {Baddeley, Adrian J. and M{\o}ller, Jesper and Waagepetersen, Rasmus Plenge},
-doi = {10.1111/1467-9574.00144},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Baddeley, M{\o}ller, Waagepetersen - 2000 - Non- and semi-parametric estimation of interaction in inhomogeneous point patterns(2).pdf:pdf},
-journal = {Statistica Neerlandica},
-number = {3},
-pages = {329--350},
-title = {{Non- and semi-parametric estimation of interaction in inhomogeneous point patterns}},
-url = {http://www.blackwell-synergy.com/links/doi/10.1111/1467-9574.00144},
-volume = {54},
-year = {2000}
-}
-@article{Morgan2013,
-abstract = {Accurate estimation of biological diversity in environmental DNA samples using high-throughput amplicon pyrosequencing must account for errors generated by PCR and sequencing. We describe a novel approach to distinguish the underlying sequence diversity in environmental DNA samples from errors that uses information on the abundance distribution of similar sequences across independent samples, as well as the frequency and diversity of sequences within individual samples. We have further refined this approach into a bioinformatics pipeline, Amplicon Pyrosequence Denoising Program (APDP) that is able to process raw sequence datasets into a set of validated sequences in formats compatible with commonly used downstream analyses packages. We demonstrate, by sequencing complex environmental samples and mock communities, that APDP is effective for removing errors from deeply sequenced datasets comprising biological and technical replicates, and can efficiently denoise single-sample datasets. APDP provides more conservative diversity estimates for complex datasets than other approaches; however, for some applications this may provide a more accurate and appropriate level of resolution, and result in greater confidence that returned sequences reflect the diversity of the underlying sample.},
-author = {Morgan, Matthew J. and Chariton, Anthony A. and Hartley, Diana M. and Court, Leon N. and Hardy, Christopher M.},
-doi = {10.1371/journal.pone.0071974},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Morgan et al. - 2013 - Improved Inference of Taxonomic Richness from Environmental DNA.pdf:pdf},
-journal = {PLoS ONE},
-number = {8},
-pages = {e71974},
-title = {{Improved Inference of Taxonomic Richness from Environmental DNA}},
-url = {onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2005.tb02393.x/},
-volume = {8},
-year = {2013}
-}
-@article{Sutton1997,
-abstract = {This paper traces the time series ("Growth of Firms") tradition in the study of market structure, and looks at how recent studies on entry and the size distribution of firms have modified thinking in this area.},
-author = {Sutton, John},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sutton - 1997 - Gibrat's Legacy.pdf:pdf},
-journal = {Journal of Economic Literature},
-number = {1},
-pages = {40--59},
-title = {{Gibrat's Legacy}},
-url = {http://econpapers.repec.org/article/aeajeclit/v{\_}3a35{\_}3ay{\_}3a1997{\_}3ai{\_}3a1{\_}3ap{\_}3a40-59.htm},
-volume = {35},
-year = {1997}
-}
-@article{TerSteege2003,
-abstract = {Large-scale patterns of Amazonian biodiversity have until now been obscured by a sparse and scattered inventory record. Here we present the first comprehensive spatial model of tree $\alpha$-diversity and - density in Amazonian rainforests, based on the largest-yet compilation of forest inventories and bolstered by a spatial interpolation technique that allows us to estimate diversity and density in areas that have never been inventoried. These data were then compared to continent-wide patterns of rainfall seasonality. We find that dry season length, while only weakly correlated with average tree $\alpha$-diversity, is a strong predictor of tree density and of maximum tree $\alpha$-diversity. The most diverse forests for any given dry season length are concentrated in a narrow latitudinal band just south of the equator, while the least diverse forests for any given dry season length are found in the Guayana Shield and Amazonian Bolivia. Denser forests are more diverse than sparser forests, even when we used a measure of diversity that corrects for sample size. We propose that rainfall seasonality regulates tree $\alpha$-diversity and -density by affecting shade tolerance and subsequently the number of different functional types of trees that can persist in an area.},
-author = {ter Steege, Hans and Pitman, Nigel and Sabatier, Daniel and van der Hout, Peter and Daly, Douglas C. and Silveira, Marcos and Phillips, Oliver L. and Vasquez, Rodolfo and van Andel, Tinde R. and Duivenvoorden, Joost F. and {Adalardo de Oliveira}, Alexandre and Ek, Renske and Lilwah, Ramesh and Thomas, Raquel and van Essen, Jessica and Baider, Claudia and Maas, Paul and Mori, Scott and Terborgh, John and {Nu{\~{n}}ez Vargas}, Percy and Mogoll{\'{o}}n, Hugo F. and Morawetz, Wilfried},
-doi = {10.1023/A:1024593414624},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/ter Steege et al. - 2003 - A spatial model of tree $\alpha$-diversity and -density for the Amazon.pdf:pdf},
-journal = {Biodiversity and Conservation},
-pages = {2255--2277},
-title = {{A spatial model of tree $\alpha$-diversity and -density for the Amazon}},
-url = {https://link.springer.com/article/10.1023/A:1024593414624},
-volume = {12},
-year = {2003}
-}
-@article{Liu2001,
-abstract = {The behaviour of five statistics (extensions of Pielou's, Clark and Evans', Pollard's, Johnson {\&} Zimmer's, and Eberhardt's statistics, which are denoted as Pi, Ce, Po' J and Eb respectively) that involve the distance from a random point to itsjth nearest neighbour were examined against several alternative patterns (lattice-based regular, inhomogeneous ran- dom, and Poisson cluster patterns) through Monte Carlo simula- tion to test their powers to detect patterns. The powers of all the five statistics increase as distance order j increases against inhomogeneous random pattern. They decrease for Pi and Ce and increase for Po, Jz, and E, against regular and Poisson cluster patterns. P, Jz, and Eb can reach high powers with the third or higher order distances in most cases. However, Po is recommended because no extra informa- tion is needed, it can reach a high power with the second or third distance even though the sample size is not large in most cases, and the test can be performed with an approximate x2 distribution associated with it. When a regular pattern is expected, J{\_} is recommended because it is more sensitive to lattice-based regular pattern than Po and Eb, especially for the first distance. However, simulation tests should be used because the speed of convergence of Jz to normal distribution is very slow.},
-annote = {Times Cited: 5},
-author = {Liu, Canran},
-doi = {10.2307/3236855},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Liu - 2001 - A comparison of five distance-based methods for spatial pattern analysis.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {3},
-pages = {411--416},
-title = {{A comparison of five distance-based methods for spatial pattern analysis}},
-volume = {12},
-year = {2001}
-}
-@article{Engen1996,
-abstract = {This paper deals with a new class of stochastic species abundance models where the abundances are the points of an inhomogeneous Poisson process. These models are the result of a dynamic approach in which the changes in abundances through time are described by a multivariate diffusion and speciation constitutes a homogeneous Poisson process. In particular, the lognormal model is generated by assuming that the density regulation within each species is given by the Gompertz curve and that the environmental variances are constant. A substantial generalization is obtained by introducing a general type of interspecific density regulation and correlated environmental noise. This more general mechanism also generates the lognormal species abundance distribution.},
-author = {Engen, Steinar and Lande, Russell},
-doi = {10.1016/0025-5564(95)00054-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Engen, Lande - 1996 - Population dynamic models generating the lognormal species abundance distribution.pdf:pdf},
-journal = {Mathematical Biosciences},
-number = {2},
-pages = {169--183},
-title = {{Population dynamic models generating the lognormal species abundance distribution}},
-url = {http://www.sciencedirect.com/science/article/pii/0025556495000542},
-volume = {132},
-year = {1996}
-}
-@article{Berg1994,
-abstract = {Quercus laevis (turkey oak) and Q. margaretta (scrubby post oak) are important scrub oaks in the sandhills forest communities of the coastal plain of the SE USA. Allozyme loci and Ripley's L-statistics were used to examine clonal structure and spatial dispersion of these species near Aiken, South Carolina. Q. laevis {\textgreater}1.5 m tall were randomly dispersed on a scale of 0-40 m, while smaller individuals were clustered on a scale of 0-12 m. Larger individuals separated by less than or equal to 1 m had 15{\%} probability of being ramets of the same clone. Q. margaretta showed strong clustering on a scale of 0- 20 m. Stems separated by less than or equal to 1 m had a 71{\%} probability of being ramets of the same clone. Clonal offspring were strongly clustered about the presumed clonal parent: 50{\%} fell within 0.50 m of this individual. Simulation modelling and direct comparison of adult and juvenile genotypes indicated that acorns are dispersed on a scale of tens of metres for both species, suggesting animal vectors such as squirrels or blue jays.},
-author = {Berg, Edward E. and Hamrick, J. L.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Berger, Parker - 1970 - Diversity of planktonic foraminifera in deep-sea sediments.pdf:pdf},
-journal = {American Journal of Botany},
-number = {1},
-pages = {7--14},
-title = {{Spatial and genetic structure of two sandhills oaks: Quercus laevis and Quercus margaretta (Fagaceae)}},
-url = {https://www.jstor.org/stable/2445556},
-volume = {81},
-year = {1994}
-}
-@article{Delgado2016,
-abstract = {Clusters are geographic concentrations of industries related by knowledge, skills, inputs, demand and/or other linkages. There is an increasing need for cluster-based data to support research, facilitate comparisons of clusters across regions and support policymakers in defining regional strategies. This article develops a novel clustering algorithm that systematically generates and assesses sets of cluster definitions (i.e., groups of closely related industries). We implement the algorithm using 2009 data for U.S. industries (six-digit NAICS), and propose a new set of benchmark cluster definitions that incorporates measures of inter-industry linkages based on co-location patterns, input–output links, and similarities in labor occupations. We also illustrate the algorithm's ability to compare alternative sets of cluster definitions by evaluating our new set against existing sets in the literature. We find that our proposed set outperforms other methods in capturing a wide range of inter-industry linkages, including the grouping of industries within the same three-digit NAICS.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Delgado, Mercedes and Porter, Michael E. and Stern, Scott},
-doi = {10.1093/jeg/lbv017},
-eprint = {arXiv:1011.1669v3},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Delgado, Porter, Stern - 2016 - Defining clusters of related industries.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {1},
-pages = {1--38},
-title = {{Defining clusters of related industries}},
-volume = {16},
-year = {2016}
-}
-@article{Andaluz2002,
-abstract = {There is a certain degree of consensus that economic activity is more concentrated in the US than in Europe. In this paper we aim to test the empirical validity of such a proposition, identifying the sectors for which this assertion is more appropriate and determining their predictable future evolution. There are three main results. First, that the US economic area is not clearly more concentrated than that of Europe; second, that the economic landscape of the European regions is changing more rapidly than that of the US states; third, that the future evolution of both economic areas will lead to an increase in the European concentrating forces and a decrease in those of the US.},
-author = {Andaluz, Joaqu{\'{i}}n and Lanaspa, Luis Fernando and Sanz, Fernando},
-doi = {10.1080/00343400220131106},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Andaluz, Lanaspa, Sanz - 2002 - Geographical Dynamics A Sectoral Comparison Between the Economic Landscapes of the United States and Eur.pdf:pdf},
-journal = {Regional Studies},
-number = {4},
-pages = {321--332},
-title = {{Geographical Dynamics: A Sectoral Comparison Between the Economic Landscapes of the United States and Europe}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/00343400220131106},
-volume = {36},
-year = {2002}
-}
-@article{Lorenz1905,
-author = {Lorenz, M. O.},
-journal = {Quarterly Publications of the American Statistical Association},
-pages = {209--219},
-title = {{Methods of Measuring the concentration of Wealth}},
-volume = {9},
-year = {1905}
-}
-@article{Peterson2013,
-abstract = {Aim Species' distributional responses to cool periods in the Pleistocene appear to have been diverse, but patterns of response are poorly known globally, and the nature of distributional responses to interglacial conditions remains largely unknown. The aim of this contribution is to assess distributional responses of forest bird species to Last Interglacial (LIG) and Last Glacial Maximum (LGM) conditions within nine forest regions world-wide, to test whether different regions experienced consistently different types of distributional responses. Location Global. Methods We use ecological niche modelling approaches under an assumption of ecological niche conservatism to assess degrees of fragmentation of species distributions through the LIG–LGM–present transitions. Models trained under present-day conditions were transferred to Pleistocene conditions, and fragmentation of potential distributional areas was assessed using FragStats. Results Our results showed four regions to have greater fragmentation at LGM than at LIG or at present; three showed greater connectivity at LGM; and two were equivocal. Main conclusions Our results suggest that the world is a patchwork of regions in which forest species experienced either consistently greater or consistently lesser population subdivision during the alternating cool and warm periods that characterized the Pleistocene. Speciation timing and dynamics should differ dramatically among major regions and biomes if these periods of connection and disjunction translate into speciation opportunity.},
-author = {Peterson, A. Townsend and Ammann, Caspar M.},
-doi = {10.1111/geb.12010},
-journal = {Global Ecology and Biogeography},
-number = {5},
-pages = {596--606},
-title = {{Global patterns of connectivity and isolation of populations of forest bird species in the late Pleistocene}},
-volume = {22},
-year = {2013}
-}
-@article{Cousins1991,
-abstract = {Species are by definition different from each other. This fact favours ranking rather than additive indices. In addition, new methods show how the degree of difference between species can be included in an index. The functional aspect of species diversity measurement is strengthened by incorporating other differences between species (such as body size, predator or parasite) as a component of diversity. The choice of index and measurement of diversity are influenced by these developments.},
-annote = {Cited By (since 1996): 63
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: TREEE
-Language of Original Document: English
-Correspondence Address: Cousins, S.H.; IERC, Cranfield Institute of Technology, Cranfield, Bedfordshire MK43 0AL, United Kingdom},
-author = {Cousins, Steven H.},
-doi = {10.1016/0169-5347(91)90212-G},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cousins - 1991 - Species diversity measurement Choosing the right index.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-number = {6},
-pages = {190--192},
-title = {{Species diversity measurement: Choosing the right index}},
-url = {http://www.sciencedirect.com/science/article/pii/016953479190212G},
-volume = {6},
-year = {1991}
-}
-@article{Deblauwe2012,
-abstract = {BACKGROUND: Independence between observations is a standard prerequisite of traditional statistical tests of association. This condition is, however, violated when autocorrelation is present within the data. In the case of variables that are regularly sampled in space (i.e. lattice data or images), such as those provided by remote-sensing or geographical databases, this problem is particularly acute. Because analytic derivation of the null probability distribution of the test statistic (e.g. Pearson's r) is not always possible when autocorrelation is present, we propose instead the use of a Monte Carlo simulation with surrogate data. METHODOLOGY/PRINCIPAL FINDINGS: The null hypothesis that two observed mapped variables are the result of independent pattern generating processes is tested here by generating sets of random image data while preserving the autocorrelation function of the original images. Surrogates are generated by matching the dual-tree complex wavelet spectra (and hence the autocorrelation functions) of white noise images with the spectra of the original images. The generated images can then be used to build the probability distribution function of any statistic of association under the null hypothesis. We demonstrate the validity of a statistical test of association based on these surrogates with both actual and synthetic data and compare it with a corrected parametric test and three existing methods that generate surrogates (randomization, random rotations and shifts, and iterative amplitude adjusted Fourier transform). Type I error control was excellent, even with strong and long-range autocorrelation, which is not the case for alternative methods. CONCLUSIONS/SIGNIFICANCE: The wavelet-based surrogates are particularly appropriate in cases where autocorrelation appears at all scales or is direction-dependent (anisotropy). We explore the potential of the method for association tests involving a lattice of binary data and discuss its potential for validation of species distribution models. An implementation of the method in Java for the generation of wavelet-based surrogates is available online as supporting material.},
-author = {Deblauwe, Vincent and Kennel, Pol and Couteron, Pierre},
-doi = {10.1371/journal.pone.0048766},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Deblauwe, Kennel, Couteron - 2012 - Testing pairwise association between spatially autocorrelated variables a new approach using surroga.pdf:pdf},
-journal = {PloS one},
-number = {11},
-pages = {e48766},
-title = {{Testing pairwise association between spatially autocorrelated variables: a new approach using surrogate lattice data.}},
-url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3492436{\&}tool=pmcentrez{\&}rendertype=abstract},
-volume = {7},
-year = {2012}
-}
-@article{Interface1964,
-author = {{Farrell, B. D., Mitter}, C. and Futuyma, D. J.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Farrell, B. D., Mitter, Futuyma - 1964 - Diversification at the Insights from phylogenetics.pdf:pdf},
-journal = {Bioscience},
-number = {1},
-pages = {34--42},
-title = {{Diversification at the Insights from phylogenetics}},
-volume = {42},
-year = {1964}
-}
-@article{Cutrini2009,
-abstract = {Localization of economic activities is a manifestation of two closely-related economic phenomena: the specialization of geographical units and the spatial concentration of industries. Nonetheless, the direction of changes in concentration and specialization, across national boundaries, may differ from those occurring within countries. Combining a regional approach with an international perspective, the paper introduces an entropy index of overall localization that allows specialization to be conceptualized as the mirror image of concentration, and also focuses attention on the possible divergence in agglomeration patterns at the different spatial scales.},
-author = {Cutrini, Eleonora},
-doi = {10.1016/j.regsciurbeco.2008.08.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cutrini - 2009 - Using entropy measures to disentangle regional from national localization patterns.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {2},
-pages = {243--250},
-title = {{Using entropy measures to disentangle regional from national localization patterns}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046208001099},
-volume = {39},
-year = {2009}
-}
-@article{Marcon2012,
-abstract = {We generalize Ripley's K function to get a new function, M, to characterize the spatial structure of a point pattern relatively to another one. We show that this new approach is pertinent in ecology when space is not homogenous and the size of objects matters. We present how to use the function and test the data against the null hypothesis of independence between points. In a tropical tree data set we detect intraspecific aggregation and interspecific competition.},
-author = {Marcon, Eric and Puech, Florence and Traissac, St{\'{e}}phane},
-doi = {10.1155/2012/619281},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech, Traissac - 2012 - Characterizing the Relative Spatial Structure of Point Patterns.pdf:pdf},
-journal = {International Journal of Ecology},
-number = {Article ID 619281},
-pages = {11},
-title = {{Characterizing the Relative Spatial Structure of Point Patterns}},
-url = {http://www.hindawi.com/journals/ijecol/2012/619281/},
-volume = {2012},
-year = {2012}
-}
-@article{Pelissier2002,
-abstract = {Spatial relationships between tree species and hydrological soil constraints are analysed within a 10-ha rain forest plot at Piste de St Elie in French Guiana. We used canonical correlation analysis to cross directly the occurrence-by- species table of 4 992 individuals (d.b.h.more than or equal to 10 cm) belonging to 120 species with qualitative soil variables and quantitative spatial data. Firstly, the list of species occurrences was confronted to nine soil descriptors characterising a weathering sequence from the initial well- drained ferralitic cover to transformed hydromorphic soil conditions. This analysis revealed that, apart from some specialised species restricted to the swamps that experience prolonged water saturation, the most abundant species can be ordered along two intermingled gradients of tolerance limiting their niche amplitude: a main gradient of tolerance to prolonged water saturation that appears down slope during the weathering sequence; a second gradient of less importance, displaying the species intolerant of prolonged water saturation according to their tolerance to temporary confinement of the uphill transformed soil systems due to the late appearance of a perched water-table. The results support the hypothesis that at Piste de St Elie, the constraining soil conditions imposed by surface water saturation are more important determinants for tree zonation of many tree species than water shortage. Secondly, the list of species occurrences was confronted to a spatial data table built from a trend surface regression of the tree coordinates. This analysis indicated that soil drainage is the main structuring factor of the local multispecies spatial pattern. After partialling out the soil effect, the multispecies pattern revealed a broader scale of heterogeneity that we supposed to be linked to endogenous factors resulting from population dynamics. Implications of the results are then discussed in the perspective of future research on tree zonation, local diversity pattern and community structuring in tropical rainforests.},
-author = {P{\'{e}}lissier, Rapha{\"{e}}l and Dray, St{\'{e}}phane and Sabatier, Daniel},
-doi = {10.1023/A:1020399603500},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/P{\'{e}}lissier, Dray, Sabatier - 2002 - Within-plot relationships between tree species occurrences and hydrological soil constraints an examp.pdf:pdf},
-journal = {Plant Ecology},
-number = {2},
-pages = {143--156},
-title = {{Within-plot relationships between tree species occurrences and hydrological soil constraints: an example in French Guiana investigated through canonical correlation analysis}},
-url = {http://link.springer.com/article/10.1023{\%}2FA{\%}3A1020399603500},
-volume = {162},
-year = {2002}
-}
-@article{Furuichi2004,
-author = {Furuichi, S. and Yanagi, K. and Kuriyama, K.},
-doi = {10.1063/1.1805729},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Furuichi, Yanagi, Kuriyama - 2004 - Fundamental properties of Tsallis relative entropy.pdf:pdf},
-journal = {Journal of Mathematical Physics},
-number = {12},
-pages = {4868--4877},
-title = {{Fundamental properties of Tsallis relative entropy}},
-url = {http://dx.doi.org/10.1063/1.1805729},
-volume = {45},
-year = {2004}
-}
-@article{Arrhenius1921,
-author = {Arrhenius, Olof},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Arrhenius - 1921 - Species and Area.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {95--99},
-title = {{Species and Area}},
-url = {http://links.jstor.org/sici?sici=0022-0477(192109)9:1{\%}3C95:SAA{\%}3E2.0.CO;2-H},
-volume = {9},
-year = {1921}
-}
-@article{Hui2007,
-abstract = {The shapes of interspecific range-size distributions at scales finer than the geographic range are highly variable. However, no numerical model has been developed as a basis for understanding this variation. Using self-similarity conditions, we present an occupancy probability transition (OPT) model to investigate the effect of sampling scale (i.e. sample grain) and species saturation (strongly positively correlated with the fractal dimension) on the shape of occupancy frequency distributions (fine scale expression of range-size distributions). In accordance with empirical observations, the model showed that core-modes are likely to be rare in occupancy frequency distributions. The modal occupancy shifted from core to satellite with an increase in sample grain (from coarse scale to fine scale) at a linear rate after log-transformation of occupancy. Saturation coefficients above a particular threshold generated multimodality. Bimodal distributions arose from a combination of different occupancy probability distributions (OPDs), with species-specific saturation coefficients generating occupancy frequency distributions of the shape commonly observed empirically, i.e. bimodal with a dominant satellite mode. This is a consequence of the statistical properties of the OPD, and is also largely insensitive to species richness. The OPT model thus provides a null model for the shape of occupancy frequency distributions. Furthermore, it demonstrates that the sample grain of a study, sampling adequacy (based on a linear sampling assumption) and the distribution of species saturation coefficients in a community are together largely able to explain the patterns observed in empirical occupancy frequency distributions. {\textcopyright} 2006 Elsevier Inc. All rights reserved.},
-author = {Hui, Cang and McGeoch, Melodie A.},
-doi = {10.1016/j.tpb.2006.07.007},
-journal = {Theoretical Population Biology},
-number = {1},
-pages = {61--70},
-title = {{A self-similarity model for the occupancy frequency distribution}},
-volume = {71},
-year = {2007}
-}
-@article{Loosmore2006,
-abstract = {Spatial point pattern analysis provides a statistical method to compare an observed spatial pattern against a hypothesized spatial process model. The G statistic, which considers the distribution of nearest neighbor distances, and the K statistic, which evaluates the distribution of all neighbor distances, are commonly used in such analyses. One method of employing these statistics involves building a simulation envelope from the result of many simulated patterns of the hypothesized model. Specifically, a simulation envelope is created by calculating, at every distance, the minimum and maximum results computed across the simulated patterns. A statistical test is performed by evaluating where the results from an observed pattern fall with respect to the simulation envelope. However, this method, which differs from P. Diggle's suggested approach, is invalid for inference because it violates the assumptions of Monte Carlo methods and results in incorrect type I error rate performance. Similarly, using the simulation envelope to estimate the range of distances over which an observed pattern deviates from the hypothesized model is also suspect. The technical details of why the simulation envelope provides incorrect type I error rate performance are described. A valid test is then proposed, and details about how the number of simulated patterns impacts the statistical significance are explained. Finally, an example of using the proposed test within an exploratory data analysis framework is provided.},
-annote = {Loosmore, N. Bert Ford, E. David},
-author = {Loosmore, N. B. and Ford, E. D.},
-doi = {10.1890/001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Loosmore, Ford - 2006 - Statistical inference using the G or K point pattern spatial statistics.pdf:pdf},
-journal = {Ecology},
-number = {8},
-pages = {1925--1931},
-title = {{Statistical inference using the G or K point pattern spatial statistics}},
-volume = {87},
-year = {2006}
-}
-@article{Shen2013b,
-abstract = {Spatially explicit consideration of species distribution can significantly add to our understanding of species coexistence. In this paper, we evaluated the relative importance of habitat heterogeneity and other clustering processes (e.g., dispersal limitation, collectively called the non-habitat clustering process) in explaining the spatial distribution patterns of 341 tree species in three stem-mapped 25–50 ha plots of tropical, subtropical, and temperate forests. Their relative importance was estimated by a method that can take one mechanism into account when estimating the effects of the other mechanism and vice versa. Our results demonstrated that habitat heterogeneity was less important in explaining the observed species patterns than other clustering processes in plots with flat topography but was more important in one of the three plots that had a complex topography. Meanwhile, both types of clustering mechanisms (habitat or non-habitat) were pervasive among species at the 50-ha scale across the studied plots. Our analyses also revealed considerable variation among species in the relative importance of the two types of mechanism within each plot and showed that this species-level variation can be partially explained by differences in dispersal mode and growth form of species in a highly heterogeneous environment. Our findings provide new perspectives on the formation of species clustering. One important finding is that a significant species– habitat association does not necessarily mean that the habitat heterogeneity has a decisive influence on species distribution. The second insight is that the large species-level variation in the relative importance of the two types of clustering mechanisms should not be ignored. Non- habitat clustering processes can play an important role on species distribution.},
-author = {Shen, Guochun and He, Fangliang and Waagepetersen, Rasmus and Sun, I-Fang and Hao, Zhanqing and Chen, Zueng-Sang and Yu, Mingjian},
-doi = {10.1890/12-1983.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Shen et al. - 2013 - Quantifying effects of habitat heterogeneity and other clustering processes on spatial distributions of tree specie.pdf:pdf},
-journal = {Ecology},
-number = {11},
-pages = {2436--2443},
-title = {{Quantifying effects of habitat heterogeneity and other clustering processes on spatial distributions of tree species}},
-url = {http://dx.doi.org/10.1890/12-1983.1},
-volume = {94},
-year = {2013}
-}
-@article{Kraft2008,
-abstract = {It is debated whether species-level differences in ecological strategy, which play a key role in much of coexistence theory, are important in structuring highly diverse communities. We examined the co-occurrence patterns of over 1100 tree species in a 25-hectare Amazonian forest plot in relation to field-measured functional traits. Using a null model approach, we show that co-occurring trees are often less ecologically similar than a niche-free (neutral) model predicts. Furthermore, we find evidence for processes that simultaneously drive convergence and divergence in key aspects of plant strategy, suggesting that at least two distinct niche-based processes are occurring. Our results show that strategy differentiation among species contributes to the maintenance of diversity in one of the most diverse tropical forests in the world.},
-author = {Kraft, Nathan J. B. and Valencia, Renato and Ackerly, David D.},
-doi = {10.1126/science.1160662},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kraft, Ackerly - 2010 - Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest.pdf:pdf},
-journal = {Science},
-number = {5901},
-pages = {580--582},
-title = {{Functional Traits and Niche-Based Assembly in an Amazonian Forest Tree Community}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/18948539},
-volume = {322},
-year = {2008}
-}
-@article{Crozier1997,
-abstract = {A variety of phylogenetic measures have been proposed to quantify distinctive- ness, often held to mark species of high conservation worth. However, distinc- tiveness of species and their numbers have different implications for conservation policy, depending on whether moral, esthetic, or utilitarian reasons are accepted as justifying conservation. The utilitarian position values species according to in- creasing numbers, and as they are more, as opposed to less, distinctive. The view is taken that conservation should seek to maximize the preserved information of the planet's biota, best expressed in terms of genetic information held in genes and not in portions of the genome of uncertain or no function. Gene number is thus an important component of assessing conservation value. Phylogenetic measures are better indicators of conservationworth than species richness, and measures using branch-lengths are better than procedures relying solely on topology. Distance measures estimating the differences between genomes are preferable to substitu- tion distances. Higher-taxon richness is a promising surrogate for branch-length measures. Complete enumeration of biotas in terms of phylogeny is desirable to avoid uncertainties in the use of indicator groups, and this is achievable now for bacteria. Phylogenetic measures are already important for management of sets of populations within species and are applicable for sets of species. Measures incorporating extinction probabilities and decision costs are being developed, and these, in conjunction with the use of confidence limits on the conservation worth of alternative reserves, are vital for conservation decision-making.},
-author = {Crozier, R. H.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Crozier - 1997 - Preserving the Information Content of Species Genetic Diversity , Phylogeny , and Conservation Worth Interaction with R.pdf:pdf},
-journal = {Annual Review of Ecology and Systematics},
-pages = {243--268},
-title = {{Preserving the Information Content of Species: Genetic Diversity , Phylogeny , and Conservation Worth Interaction with Reasons Justifying the Preservation}},
-volume = {28},
-year = {1997}
-}
-@article{Tuomisto2010a,
-abstract = {The term beta diversity has been used to refer to a wide variety of phenomena. Although all of these encompass some kind of compositional heterogeneity between places, many are not related to each other in any predictable way. The present two-part review aims to put the different phenomena that have been called a beta component of diversity into a common conceptual framework, and to explain what each of them measures. In this first part, the focus is on defining beta diversity. This involves deciding what diversity is and how the observed total or gamma diversity (gamma) is partitioned into alpha (alpha) and beta (beta) components. Several different definitions of "beta diversity" that result from these decisions have been used in the ecological literature. True beta diversity is obtained when the total effective number of species in a dataset (true gamma diversity gamma) is multiplicatively partitioned into the effective number of species per compositionally distinct virtual sampling unit (true alpha diversity alpha(d)) and the effective number of such compositional units (beta(Md)=gamma/alpha(d)). All true diversities quantify the effective number of types of entities. Because the other variants of "beta diversity" that have been used by ecologists quantify other phenomena, an alternative nomenclature is proposed here for the seven most popular beta components: regional-to-local diversity ratio, two-way diversity ratio, absolute effective species turnover (=regional diversity excess), Whittaker's effective species turnover, proportional effective species turnover, regional entropy excess and regional variance excess. In the second part of the review, the focus will be on how to quantify these phenomena in practice. This involves deciding how the sampling units that contribute to total diversity are selected, and whether the entity that is quantified is all of "beta diversity", a specific part of "beta diversity", the rate of change in "beta diversity" in relation to a given external factor, or something else.},
-annote = {Tuomisto, Hanna},
-author = {Tuomisto, Hanna},
-doi = {10.1111/j.1600-0587.2009.05880.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tuomisto - 2010 - A diversity of beta diversities straightening up a concept gone awry. Part 1. Defining beta diversity as a function of.pdf:pdf},
-journal = {Ecography},
-number = {1},
-pages = {2--22},
-title = {{A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2009.05880.x/abstract},
-volume = {33},
-year = {2010}
-}
-@article{Glaeser1999,
-abstract = {Alfred Marshall argues that industrial agglomerations exist in part because individuals learn from each other when they live and work in close proximity, and increasing amounts of evidence confirms this. This paper formalizes Marshall's theory in a model where individuals acquire skills by interacting with one another, and dense urban areas increase the speed of interactions. The model predicts that cities will have a higher mean and higher variance of skills, and will attract young people who are not too risk averse and who benefit most from learning e.g., more patient people . Urbanization will rise when the returns to skills rise, when the ability to learn by imitation rises, and when the level of health in the economy rises.},
-author = {Glaeser, Edward L.},
-doi = {10.1006/juec.1998.2121},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Glaeser - 1999 - Learning in Cities.pdf:pdf},
-journal = {Journal of Urban Economics},
-number = {2},
-pages = {254--277},
-title = {{Learning in Cities}},
-url = {http://www.sciencedirect.com/science/article/pii/S0094119098921210},
-volume = {46},
-year = {1999}
-}
-@article{Bonachela2008,
-abstract = {Estimating entropies from limited data series is known to be a non-trivial task. Na{\"{i}}ve estimations are plagued with both systematic (bias) and statistical errors. Here, we present a new 'balanced estimator' for entropy functionals (Shannon, R{\'{e}}nyi and Tsallis) specially devised to provide a compromise between low bias and small statistical errors, for short data series. This new estimator outperforms other currently available ones when the data sets are small and the probabilities of the possible outputs of the random variable are not close to zero. Otherwise, other well-known estimators remain a better choice. The potential range of applicability of this estimator is quite broad specially for biological and digital data series.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Bonachela, Juan A. and Hinrichsen, Haye and Mu{\~{n}}oz, Miguel A.},
-doi = {10.1088/1751-8113/41/20/202001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonachela, Hinrichsen, Mu{\~{n}}oz - 2008 - Entropy estimates of small data sets.pdf:pdf},
-journal = {Journal of Physics A: Mathematical and Theoretical},
-number = {202001},
-pages = {1--9},
-title = {{Entropy estimates of small data sets}},
-url = {http://stacks.iop.org/1751-8121/41/i=20/a=202001},
-volume = {41},
-year = {2008}
-}
-@article{Rozas2003,
-abstract = {Past regeneration patterns of Quercus robur L. and Fagus sylvatica L. and their relationship to canopy structure, disturbances and forest-use history were investigated in an old-growth, lowland forest in Cantabria, Northern Spain. Dendroecological techniques were used to estimate tree ages and reconstruct disturbance histories in four representative stands which differed in composition and structure. Age estimates and tree locations were used to reconstruct patterns of tree establishment. Documentary sources were also used to report on changes in land-use during the past 250 years. Age structures of both species were discontinuous in time and space, and revealed two main cohorts distributed in even-aged, spatially segregated patches. Juveniles showed a clumped spatial pattern at varying distances, indicating an establishment: in more or less extensive patches. Establishment site analyses revealed that Q. robur regenerated in canopy gaps, while F. sylvatica recruited throughout the forest floor, but it displayed inhibition near mature conspecifics. A lack of tree establishment from the 1840s to the 1920s coincided with an intense grazing pressure from domestic animals. F. sylvatica exhibited continuous recruitment in periods of forest protection against grazing, such as from the 1740s to the 1830s and from the 1920s. By contrast, Q. robur recruitment was dependent on both low grazing intensities and disturbances that resulted in the expansion of existing canopy openings, as occurred in 1943, 1956 and 1967. Past selective cuttings, canopy closure and forest protection could be responsible for the increasing decline of oak dominance. Planting Q. robur and controlling F. sylvatica regeneration are therefore advisable to prevent the complete domination of beech in the future forest canopy. (C) 2003 Elsevier Science B.V All rights reserved.},
-author = {Rozas, V.},
-doi = {10.1016/S0378-1127(03)00070-7},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Rozas - 2003 - Regeneration patterns, dendroecology, and forest-use history in an old-growth beech-oak lowland forest in Northern Spain.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {175--194},
-title = {{Regeneration patterns, dendroecology, and forest-use history in an old-growth beech-oak lowland forest in Northern Spain}},
-volume = {182},
-year = {2003}
-}
-@article{Gambette2011,
-abstract = {Given a simple undirected weighted or unweighted graph, we try to cluster the vertex set into communities and also to quantify the robustness of these clusters. For that task, we propose a new method, called bootstrap clustering which consists in (i) defining a new clustering algorithm for graphs, (ii) building a set of graphs similar to the initial one, (iii) applying the clustering method to each of them, making a profile (set) of partitions, (iv) computing a consensus partition for this profile, which is the final graph partitioning. This allows to evaluate the robustness of a cluster as the average percentage of partitions in the profile joining its element pairs ; this notion can be extended to partitions. Doing so, the initial and consensus partitions can be compared. A simulation protocol, based on random graphs structured in communities is designed to evaluate the efficiency of the Bootstrap Clustering approach.},
-author = {Gambette, Philippe and Gu{\'{e}}noche, Alain},
-doi = {10.1051/ro/2012001},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gambette, Gu{\'{e}}noche - 2011 - Bootstrap clustering for graph partitioning.pdf:pdf},
-journal = {RAIRO - Operations Research},
-number = {4},
-pages = {339--352},
-title = {{Bootstrap clustering for graph partitioning}},
-url = {http://www.rairo-ro.org/10.1051/ro/2012001},
-volume = {45},
-year = {2011}
-}
-@article{Huang2011,
-abstract = {To evaluate the originality of a species for determining its conservation priority, most indices use the branching pattern and the branch length of a phylogenetic tree to represent the diversification pattern and the number of characters. One limitation of these indices is their lack of consideration of the dynamic process, such as character changes and distribution along lineages during evolution. In this study, we propose a robust framework incorporating the underlying dynamic processes under a framework of genome evolution to model character changes and distribution along different lineages in a given phylogenetic tree. Our framework provides a more transparent modeling, instead of the simple surrogates of branching pattern and branch length previously employed. Nonrandom extinction has been found to be clustered within old and species-poor clades, thus it is desirable to combine the evaluation of originality of clades, which will provide a more complete picture and a useful tool for setting global conservation priorities. Using a phylogenetic tree consisting of 70 species of New World terrestrial Carnivora, we demonstrate that the index derived from our framework can discern the difference in originality of clades. Moreover, we demonstrate that the originality of clades and species in a tree changes with different scenarios of dynamic processes, which were neglected by previous indices. We find that the originality of clades should be one of the criteria for setting global conservation priorities. {\textcopyright} 2011 Elsevier Ltd.},
-author = {Huang, Jianxiong and Mi, Xiangcheng and Ma, Keping},
-doi = {10.1016/j.jtbi.2011.01.037},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Huang, Mi, Ma - 2011 - A genome evolution-based framework for measures of originality for clades.pdf:pdf},
-journal = {Journal of Theoretical Biology},
-number = {1},
-pages = {99--105},
-title = {{A genome evolution-based framework for measures of originality for clades}},
-url = {http://dx.doi.org/10.1016/j.jtbi.2011.01.037},
-volume = {276},
-year = {2011}
-}
-@article{Kosman1996,
-author = {Kosman, Evsey},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kosman - 1996 - Difference and diversity of plant pathogen populations a new approach for measuring.pdf:pdf},
-journal = {Phytopathology},
-number = {11},
-pages = {1152--1155},
-title = {{Difference and diversity of plant pathogen populations: a new approach for measuring}},
-url = {http://www.apsnet.org/publications/phytopathology/backissues/Documents/1996Articles/Phyto86n11{\_}1152.pdf},
-volume = {86},
-year = {1996}
-}
-@article{Miller2017,
-abstract = {Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 $\alpha$-diversity and 10 $\beta$-diversity metrics of community phylogenetic structure can be combined with nine null models (eight for $\beta$-diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual-based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 approaches against each assembly process. Many $\alpha$-diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12, and the number of unique $\alpha$-diversity approaches to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. Of $\alpha$-diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance-based metrics were best able to detect competitive exclusion. Overall, $\beta$-diversity metrics tended to outperform $\alpha$-diversity metrics, showing greater power and fewer false positives, although some $\alpha$-diversity metrics exhibited nearly comparably performance. Null model selection affected type I error rates more than metric selection. A new null model that maintains species richness, and approximately maintains occurrence frequency and abundance across plots, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.},
-author = {Miller, Eliot T. and Farine, Damien R. and Trisos, Christopher H.},
-doi = {10.1111/ecog.02070},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Miller, Farine, Trisos - 2017 - Phylogenetic community structure metrics and null models a review with new methods and software.pdf:pdf},
-journal = {Ecography},
-number = {4},
-pages = {461--477},
-title = {{Phylogenetic community structure metrics and null models: a review with new methods and software}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02070/abstract},
-volume = {40},
-year = {2017}
-}
-@article{Basset2012,
-abstract = {Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6144 arthropod species from 0.48 hectare and extrapolated total species richness to larger areas on the basis of competing models. The whole 6000-hectare forest reserve most likely sustains 25,000 arthropod species. Notably, just 1 hectare of rainforest yields {\textgreater}60{\%} of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates of arthropod biodiversity developed from plant models.},
-author = {Basset, Yves and Cizek, Lukas and Cu{\'{e}}noud, Philippe and Didham, Raphael K. and Guilhaumon, Fran{\c{c}}ois and Missa, Olivier and Novotny, Vojtech and {\O}degaard, Frode and Roslin, Tomas and Schmidl, J{\"{u}}rgen and Tishechkin, Alexey K. and Winchester, Neville N. and Roubik, David W. and Aberlenc, Henri-Pierre and Bail, Johannes and Barrios, H{\'{e}}ctor and Bridle, Jon R. and Casta{\~{n}}o-Meneses, Gabriela and Corbara, Bruno and Curletti, Gianfranco and {Duarte da Rocha}, Wesley and {De Bakker}, Domir and Delabie, Jacques H. C. and Dejean, Alain and Fagan, Laura L. and Floren, Andreas and Kitching, Roger L. and Medianero, Enrique and Miller, Scott E. and {Gama de Oliveira}, Evandro and Orivel, J{\'{e}}r{\^{o}}me and Pollet, Marc and Rapp, Mathieu and Ribeiro, S{\'{e}}rvio P. and Roisin, Yves and Schmidt, Jesper B. and S{\o}rensen, Line and Leponce, Maurice},
-doi = {10.1126/science.1226727},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Basset et al. - 2012 - Arthropod Diversity in a Tropical Forest.pdf:pdf},
-journal = {Science},
-number = {6113},
-pages = {1481--1484},
-title = {{Arthropod Diversity in a Tropical Forest}},
-url = {http://www.sciencemag.org/content/338/6113/1481.abstract},
-volume = {338},
-year = {2012}
-}
-@article{Tang2015,
-abstract = {The objective of this paper is to assess an approach to statistical modeling of point referenced establishment data that permit inclusion of “environmental” or establishment-specific covariates and specific forms of interestablishment interaction. Gibbs models are used to decompose the conditional intensity of the spatial point process into trend and interaction components. The trend is composed of access measures (primarily different classes of roads) and three different interaction processes are tested: Geyer, area interaction, and Strauss hard core. While the models used have proved to be useful in ecology, we are unaware of any applications to establishment or firm data. In empirical application, the models yield intuitively appealing results for the trend component, and the ability to specify the interaction component gives deeper insights into interestablishment spatial dynamics than any previously published methods.},
-author = {Tang, Wenwu and Feng, Wenpeng and Jia, Meijuan},
-doi = {10.1080/13658816.2014.976569},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tang, Feng, Jia - 2015 - Massively parallel spatial point pattern analysis Ripley's K function accelerated using graphics processing uni.pdf:pdf},
-journal = {International Journal of Geographical Information Science},
-number = {3},
-pages = {412--439},
-title = {{Massively parallel spatial point pattern analysis: Ripley's K function accelerated using graphics processing units}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/13658816.2014.976569},
-volume = {29},
-year = {2015}
-}
-@book{Malbos2016,
-address = {Lyon},
-author = {Malbos, Philippe},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Malbos - 2016 - Analyse matricielle et alg{\`{e}}bre lin{\'{e}}aire appliqu{\'{e}}e.pdf:pdf},
-publisher = {Universit{\'{e}} Claude Bernard, Lyon I},
-title = {{Analyse matricielle et alg{\`{e}}bre lin{\'{e}}aire appliqu{\'{e}}e}},
-url = {http://math.univ-lyon1.fr/homes-www/malbos/},
-year = {2016}
-}
-@article{Ellison2010a,
-author = {Ellison, Aaron M.},
-doi = {doi:10.1890/09-1692.1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ellison - 2010 - Partitioning diversity.pdf:pdf},
-journal = {Ecology},
-number = {7},
-pages = {1962--1963},
-title = {{Partitioning diversity}},
-url = {http://www.esajournals.org/doi/abs/10.1890/09-1692.1},
-volume = {91},
-year = {2010}
-}
-@article{Jaouen2010,
-abstract = {• In the dense tropical rainforest understorey, saplings exhibit different growth strategies aiming at reaching light levels better fitting their ecology. Investing mainly in height growth, at the expense of their width, a lot are close to mechanical instability. Tachigali melinonii, a long living heliophilic tree species, is frequently observed to be extremely slender and supported by neighbours. Such observations suggest an active growth control through the perception of mechanical environment. • Mechanical environment or light availability, which one is the most influent on growth and slenderness (H/D)? To test this question, we recorded growth of control and staked saplings of two species with contrasting habits and ecology: T. melinonii, and Dicorynia guianensis, along a natural light gradient. • Dicorynia, the more stable, responded more clearly to the staking treatment, showing slenderness increase when light is available, whereas for Tachigali, only light availability governed growth. • For Tachigali, growth allocation is mainly governed by light availability and ontogeny, whereas Dicorynia is probably similar to the average tree strategy, using the thigmomorphogenetic physiological process to control its stability.},
-author = {Jaouen, Ga{\"{e}}lle and Fournier, Meriem and Almeras, Tancr{\`{e}}de},
-doi = {10.1051/forest/2009104},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Jaouen, Fournier, Almeras - 2010 - Thigmomorphogenesis versus light in biomechanical growth strategies of saplings of two tropical rain.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {2},
-pages = {211},
-title = {{Thigmomorphogenesis versus light in biomechanical growth strategies of saplings of two tropical rain forest tree species}},
-url = {http://dx.doi.org/10.1051/forest/2009104},
-volume = {67},
-year = {2010}
-}
-@article{Basharin1959,
-abstract = {The mean value and variance are computed for a statistical estimate for the entropy of a sequence of mutually independent random variables having a similar distribution. The estimate is shown to be biased, consistent and asymptotically normal.},
-author = {Basharin, G. P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Basharin - 1959 - On a Statistical Estimate for the Entropy of a Sequence of Independent Random Variables.pdf:pdf},
-journal = {Theory of Probability and its Applications},
-number = {3},
-pages = {333--336},
-title = {{On a Statistical Estimate for the Entropy of a Sequence of Independent Random Variables}},
-url = {http://www.mathnet.ru/php/archive.phtml?wshow=paper{\&}jrnid=tvp{\&}paperid=4896{\&}option{\_}lang=eng},
-volume = {4},
-year = {1959}
-}
-@book{Hubbell2001,
-author = {Hubbell, Stephen P.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hubbell - 2001 - The unified neutral theory of biodiversity and biogeography.pdf:pdf},
-isbn = {9781400837526},
-publisher = {Princeton University Press},
-title = {{The unified neutral theory of biodiversity and biogeography}},
-year = {2001}
-}
-@article{Ricotta2017c,
-abstract = {In this paper, we examine some basic properties of the Bray-Curtis dissimilarity as compared with other distance and dissimilarity functions applied to ecological abundance data. We argue that the ability of every coefficient to measure species-level contributions is a fundamental requirement. By suggesting an additive decomposition formula for the Bray-Curtis coefficient we derive a general formula of dissimilarity, which includes the Canberra distance and the Bray-Curtis dissimilarity as special cases. A similar general formula is also proposed for the Marczewski-Steinhaus coefficient. Finally, using a modified version of Dalton's principle of transfers, we show that the Bray-Curtis coefficient and the city-block distance exhibit a linear response to the transfer of species abundances from an abundant plot to a less abundant plot. At the other extreme, the chord and the Hellinger distances show an irregular and non-monotonic behavior.},
-author = {Ricotta, Carlo and Podani, J{\'{a}}nos},
-doi = {10.1016/j.ecocom.2017.07.003},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ricotta, Podani - 2017 - On some properties of the Bray-Curtis dissimilarity and their ecological meaning.pdf:pdf},
-journal = {Ecological Complexity},
-pages = {201--205},
-title = {{On some properties of the Bray-Curtis dissimilarity and their ecological meaning}},
-url = {http://dx.doi.org/10.1016/j.ecocom.2017.07.003},
-volume = {31},
-year = {2017}
-}
-@misc{Chao2010a,
-address = {Hsin-Chu, Taiwan},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Chao, Anne and Shen, Tsung-Jen},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Shen - 2010 - Program SPADE Species Prediction And Diversity Estimation. Program and user's guide.pdf:pdf},
-publisher = {CARE},
-title = {{Program SPADE: Species Prediction And Diversity Estimation. Program and user's guide.}},
-url = {http://chao.stat.nthu.edu.tw/wordpress/wp-content/uploads/software/SPADE{\_}UserGuide.pdf},
-year = {2010}
-}
-@article{Podani1999,
-abstract = {The possibilities of calculating similarity based on ordinal characters are evaluated by distinguishing subtypes of the ordinal scale. Multivariate analysis is most problematic when ordinal variables appear together with other scale types in the data. This difficulty is solved by extending Gower's general coefficient of similarity to ordinal data types, facilitating cluster analysis and multidimensional scaling. Two alternatives, a non-metric and a metric version, are offered. The modified formula implies that ordinal variables are equally weighted with the others, and that partially and fully ranked data are both applicable, due to the inherent standardisation procedure. A morphological data set derived for the moss genus Tortula illustrates the new approach.},
-author = {Podani, J{\'{a}}nos},
-doi = {10.2307/1224438},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Podani - 1999 - Extending Gower's General Coefficient of Similarity to Ordinal Characters.pdf:pdf},
-journal = {Taxon},
-number = {2},
-pages = {331--340},
-title = {{Extending Gower's General Coefficient of Similarity to Ordinal Characters}},
-url = {http://www.jstor.org/stable/1224438},
-volume = {48},
-year = {1999}
-}
-@article{Grime2002,
-author = {Grime, J. P.},
-doi = {10.1111/j.1654-1103.2002.tb02072.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Grime - 2002 - Declining plant diversity empty niches or functional shifts.pdf:pdf},
-journal = {Journal of Vegetation Science},
-number = {4},
-pages = {457--460},
-title = {{Declining plant diversity: empty niches or functional shifts?}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2002.tb02072.x/abstract},
-volume = {13},
-year = {2002}
-}
-@article{Kunin2018,
-abstract = {The challenge of biodiversity upscaling, estimating the species richness of a large area from scattered local surveys within it, has attracted increasing interest in recent years, producing a wide range of competing approaches. Such methods, if successful, could have important applications to multi-scale biodiversity estimation and monitoring. Here we test 19 techniques using a high quality plant data set: the GB Countryside Survey 1999, detailed surveys of a stratified random sample of British landscapes. In addition to the full data set, a set of geographical and statistical subsets was created, allowing each method to be tested on multiple data sets with different characteristics. The predictions of the models were tested against the “true” species–area relationship for British plants, derived from contemporaneously surveyed national atlas data. This represents a far more ambitious test than is usually employed, requiring 5–10 orders of magnitude in upscaling. The methods differed greatly in their performance; while there are 2,326 focal plant taxa recorded in the focal region, up-scaled species richness estimates ranged from 62 to 11,593. Several models provided reasonably reliable results across the 16 test data sets: the Shen and He and the Ulrich and Ollik models provided the most robust estimates of total species richness, with the former generally providing estimates within 10{\%} of the true value. The methods tested proved less accurate at estimating the shape of the species–area relationship (SAR) as a whole; the best single method was Hui's Occupancy Rank Curve approach, which erred on average by {\textless}20{\%}. A hybrid method combining a total species richness estimate (from the Shen and He model) with a downscaling approach (the {\v{S}}izling model) proved more accurate in predicting the SAR (mean relative error 15.5{\%}) than any of the pure upscaling approaches tested. There remains substantial room for improvement in upscaling methods, but our results suggest that several existing methods have a high potential for practical application to estimating species richness at coarse spatial scales. The methods should greatly facilitate biodiversity estimation in poorly studied taxa and regions, and the monitoring of biodiversity change at multiple spatial scales.},
-author = {Kunin, William E. and Harte, John and He, Fangliang and Hui, Cang and Jobe, R. Todd and Ostling, Annette and Polce, Chiara and {\v{S}}izling, Arno{\v{s}}t and Smith, Adam B. and Smith, Krister and Smart, Simon M. and Storch, David and Tj{\o}rve, Even and Ugland, Karl-Inne and Ulrich, Werner and Varma, Varun},
-doi = {10.1002/ecm.1284},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kunin et al. - 2018 - Upscaling biodiversity estimating the species-area relationship from small samples.pdf:pdf},
-journal = {Ecological Monographs},
-title = {{Upscaling biodiversity: estimating the species-area relationship from small samples}},
-url = {http://doi.wiley.com/10.1002/ecm.1284},
-volume = {in press},
-year = {2018}
-}
-@article{Gao2013,
-abstract = {Spatial point pattern is an important tool for describing the spatial distribution of species in ecology. Negative binomial distribution (NBD) is widely used to model spatial aggregation. In this paper, we derive the probability distribution model of event-to-event nearest neighbor distance (distance from a focal individual to its n-th nearest individual). Compared with the probability distribution model of point-to-event nearest neighbor distance (distance from a randomly distributed sampling point to the n-th nearest individual), the new probability distribution model is more flexible. We propose that spatial aggregation can be detected by fitting this probability distribution model to event-to-event nearest neighbor distances. The performance is evaluated using both simulated and empirical spatial point patterns.},
-author = {Gao, Meng},
-doi = {10.1007/s11284-013-1029-x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gao - 2013 - Detecting spatial aggregation from distance sampling a probability distribution model of nearest neighbor distance.pdf:pdf},
-journal = {Ecological Research},
-number = {3},
-pages = {1--9},
-title = {{Detecting spatial aggregation from distance sampling: a probability distribution model of nearest neighbor distance}},
-url = {http://dx.doi.org/10.1007/s11284-013-1029-x},
-volume = {28},
-year = {2013}
-}
-@article{Hubbell1990,
-abstract = {We report dynamic data on the spatial pattern of sapling recruitment over a three-year interval in a 50 ha{\textless}latex{\textgreater}{\$}\backslashdagger {\$}{\textless}/latex{\textgreater} mapped plot Barro Colorado Island (BCI), Panama. We analysed sapling recruitment of a given tree species against recruitment of all other competing tree species, as a function of distance to nearest conspecific adult tree. Strong negative conspecific effects of large trees on saplings were detectable in a few very common species, but not in many others. The power to detect conspecific effects was evaluated in model tree populations in which the strength of these effects was known a priori. The measured conspecific effects appear strong enough in the densest species to prevent them from assuming complete dominance. However, many species do not show these effects, and we conclude that these effects play only a limited contributing role to the maintenance of tree species diversity in the BCI forest.},
-author = {Hubbell, S. P. and Condit, R. and Foster, R. B. and Grubb, P. J. and Thomas, C. D.},
-doi = {10.1098/rstb.1990.0198},
-issn = {0962-8436},
-journal = {Philosophical Transactions of the Royal Society B},
-number = {1257},
-pages = {269--281},
-title = {{Presence and absence of density dependence in a neotropical tree community}},
-volume = {330},
-year = {1990}
-}
-@article{Marcon2003a,
-abstract = {We propose new methods for evaluating the spatial distribution of firms. To assess whether firms are concentrated or dispersed, economists have traditionally used indices that analyse the heterogeneity of a spatial structure at a single geographic level. We introduce distance-based methods, Besag's L function (derived from Ripley's K function) and Diggle and Chetwynd's D function to describe simultaneously spatial distribution at different geographical scales. Our empirical applications consider the distribution of French manufacturing firms in the Paris area and in France generally. For some geographic levels, results show significant concentration or dispersion of firms according to their sector of activity.},
-author = {Marcon, Eric and Puech, Florence},
-doi = {10.1093/jeg/lbg016},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech - 2003 - Evaluating the geographic concentration of industries using distance-based methods.pdf:pdf},
-journal = {Journal of Economic Geography},
-number = {4},
-pages = {409--428},
-title = {{Evaluating the geographic concentration of industries using distance-based methods}},
-url = {http://joeg.oxfordjournals.org/content/3/4/409},
-volume = {3},
-year = {2003}
-}
-@incollection{Penttinen2006,
-address = {Helsinki},
-author = {Penttinen, Antti},
-booktitle = {The Yearbook of the Finnish Statistical Society},
-pages = {70--91},
-publisher = {The Finnish Statistical Society},
-title = {{Statistics for Marked Point Patterns}},
-year = {2006}
-}
-@article{Socolar2016,
-abstract = {To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity - the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. Beta-diversity reveals the spatial scaling of diversity loss. Beta-diversity illuminates mechanisms of regional diversity maintenance.Human activities cause beta-diversity to increase, decrease, or remain unchanged.Conservation significance of beta-diversity shift depends on local diversity dynamics.},
-author = {Socolar, Jacob B. and Gilroy, James J. and Kunin, William E. and Edwards, David P.},
-doi = {10.1016/j.tree.2015.11.005},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Socolar et al. - 2016 - How Should Beta-Diversity Inform Biodiversity Conservation.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-month = {jan},
-number = {1},
-pages = {67--80},
-title = {{How Should Beta-Diversity Inform Biodiversity Conservation?}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S016953471500289X},
-volume = {31},
-year = {2016}
-}
-@article{Sokal1958,
-abstract = {Starting with correlaton coefficients (based on numerous characters) among species of a systematic unit, the authors developped a method for grouping species, and regrouping the resltant assemblages, to form a classificatory hierarchy most easily expressed as a treelike diagram of relationships. The details of the method are described, using as an example a group of bees. The resulting classification was similar to that previously established ny classical systematic methods, although somes taxonomic changes were made in view of the new light thrown on relationships. The method is time consuming, although practical inisolated cases, with punched-card machines such as were used; it becomes generally practical with increasingly widely available digital computers.},
-author = {Sokal, Robert R. and Michener, C. D.},
-doi = {citeulike-article-id:1327877},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sokal, Michener - 1958 - A statistical method for evaluating systematic relationships.pdf:pdf},
-journal = {The University of Kansas Science Bulletin},
-number = {22},
-pages = {1409--1438},
-title = {{A statistical method for evaluating systematic relationships}},
-url = {https://archive.org/details/cbarchive{\_}133648{\_}astatisticalmethodforevaluatin1902},
-volume = {38},
-year = {1958}
-}
-@article{HonorioCoronado2015,
-abstract = {Aim To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.},
-author = {{Honorio Coronado}, Eur{\'{i}}dice N. and Dexter, Kyle G. and Pennington, R. Toby and Chave, J{\'{e}}r{\^{o}}me and Lewis, Simon L. and Alexiades, Miguel N. and Alvarez, Esteban and {Alves de Oliveira}, Atila and Amaral, I{\^{e}}da Le{\~{a}}o and Araujo-Murakami, Alejandro and Arets, Eric J. M. M. and Aymard, Gerardo A. and Baraloto, Christopher and Bonal, Damien and Brienen, Roel and Cer{\'{o}}n, Carlos and {Cornejo Valverde}, Fernando and {Di Fiore}, Anthony and Farfan-Rios, William and Feldpausch, Ted R. and Higuchi, Niro and Huamantupa-Chuquimaco, Isau and Laurance, Susan G. and Laurance, William F. and L{\'{o}}pez-Gonzalez, Gabriela and Marimon, Beatriz Schwantes and Marimon-Junior, Ben Hur and {Monteagudo Mendoza}, Abel and Neill, David and {Palacios Cuenca}, Walter and Pe{\~{n}}uela-Mora, Maria Cristina and Pitman, Nigel C. A. and Prieto, Adriana and Quesada, Carlos A. and {Ram{\'{i}}rez Angulo}, Hirma and Rudas, Agust{\'{i}}n and Ruschel, Ademir R. and {Salinas Revilla}, Norma and Salom{\~{a}}o, Rafael P. and {Segalin de Andrade}, Ana and Silman, Miles R. and Spironello, Wilson and ter Steege, Hans and Terborgh, John and Toledo, Marisol and {Valenzuela Gamarra}, Luis and Vieira, Ima C. G. and {Vilanova Torre}, Emilio and Vos, Vincent and Phillips, Oliver L.},
-doi = {10.1111/ddi.12357},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Honorio Coronado et al. - 2015 - Phylogenetic diversity of Amazonian tree communities.pdf:pdf},
-journal = {Diversity and Distributions},
-number = {11},
-pages = {1295--1307},
-title = {{Phylogenetic diversity of Amazonian tree communities}},
-url = {http://doi.wiley.com/10.1111/ddi.12357},
-volume = {21},
-year = {2015}
-}
-@article{Engen1974,
-abstract = {An extension of the negative binomial model as a species frequency distribution is given by allowing the shape parameter k to take values between -1 and 0. Different estimation methods are assessed for this extended negative binomial model and the logarithmic series model. Tables for standard errors are given.},
-author = {Engen, Steinar},
-doi = {10.2307/2334353},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Engen - 1974 - On Species Frequency Models.pdf:pdf},
-journal = {Biometrika},
-number = {2},
-pages = {263--270},
-title = {{On Species Frequency Models}},
-volume = {61},
-year = {1974}
-}
-@article{Maurseth2002,
-abstract = {This paper addresses the pattern of knowledge flows as indicated by patent citations between European regions. Our findings support the hypothesis that there are important barriers to knowledge flows in Europe. Patent citations occur more often between regions which belong to the same country and which are in geographical proximity. Furthermore, patent citations are industry specific and occur most often between regions that are specialised in industrial sectors with specific technological linkages between them. Patent citations are also more frequent when the citing region belongs to the same linguistic group as the cited region.},
-author = {Maurseth, Per Botolf and Verspagen, Bart},
-doi = {10.1111/1467-9442.00300},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Maurseth, Verspagen - 2002 - Knowledge Spillovers in Europe a Patent Citations Analysis.pdf:pdf},
-journal = {Scandinavian Journal of Economics},
-number = {4},
-pages = {531--545},
-title = {{Knowledge Spillovers in Europe: a Patent Citations Analysis}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9442.00300/abstract},
-volume = {104},
-year = {2002}
-}
-@article{Cressie1984,
-author = {Cressie, Noel and Read, Timothy R. C.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cressie, Read - 1984 - Multinomial Goodness-of-Fit Tests.pdf:pdf},
-journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
-number = {3},
-pages = {440--464},
-title = {{Multinomial Goodness-of-Fit Tests}},
-url = {http://www.jstor.org/stable/2345686},
-volume = {46},
-year = {1984}
-}
-@phdthesis{Ruelle2002,
-author = {Ruelle, Julien},
-publisher = {Universit{\'{e}} Montpellier II},
-title = {{Diversit{\'{e}} de bois de tension chez quelques arbres de for{\^{e}}t tropicale humide}},
-year = {2002}
-}
-@article{Chao2003,
-abstract = {A biological community usually has a large number of species with relatively small abundances. When a random sample of individuals is selected and each individual is classified according to species identity, some rare species may not be discovered. This paper is concerned with the estimation of Shannon's index of diversity when the number of species and the species abundances are unknown. The traditional estimator that ignores the missing species underestimates when there is a non-negligible number of unseen species. We provide a different approach based on unequal probability sampling theory because species have different probabilities of being discovered in the sample. No parametric forms are assumed for the species abundances. The proposed estimation procedure combines the Horvitz-Thompson (1952) adjustment for missing species and the concept of sample coverage, which is used to properly estimate the relative abundances of species discovered in the sample. Simulation results show that the proposed estimator works well under various abundance models even when a relatively large fraction of the species is missing. Three real data sets, two from biology and the other one from numismatics, are given for illustration.},
-annote = {Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713
-
-
-Cited By (since 1996):2
-Export Date: 25 March 2014
-Source: Scopus
-Art. No.: 6296713},
-author = {Chao, Anne and Shen, Tsung-Jen},
-doi = {10.1023/A:1026096204727},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Shen - 2003 - Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample.pdf:pdf},
-journal = {Environmental and Ecological Statistics},
-number = {4},
-pages = {429--443},
-title = {{Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample}},
-url = {https://link.springer.com/article/10.1023{\%}2FA{\%}3A1026096204727},
-volume = {10},
-year = {2003}
-}
-@article{Ripley1984,
-abstract = {This first correspondent's paper on spatial statistics surveys recent developments in the field, updating the author's monograph Spatial Statistics. The main themes are edge effects, multitype point processes and computation.},
-author = {Ripley, Brian D.},
-doi = {10.2307/1403097},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ripley - 1984 - Spatial Statistics Developments 1980-3.pdf:pdf},
-journal = {International Statistical Review},
-number = {2},
-pages = {141--150},
-title = {{Spatial Statistics: Developments 1980-3}},
-url = {http://www.jstor.org/stable/1403097},
-volume = {52},
-year = {1984}
-}
-@article{Boersma2016a,
-abstract = {Climate change is expected to increase climate variability and the occurrence of extreme climatic events, with potentially devastating effects on aquatic ecosystems. However, little is known about the role of climate extremes in structuring aquatic communities or the interplay between climate and local abiotic and biotic factors. Here, we examine the relative influence of climate and local abiotic and biotic conditions on biodiversity and community structure in lake invertebrates. We sampled aquatic invertebrates and measured environmental variables in 19 lakes throughout California, USA, to test hypotheses of the relationship between climate, local biotic and environmental conditions, and the taxonomic and functional structure of aquatic invertebrate communities. We found that, while local biotic and abiotic factors such as habitat availability and conductivity were the most consistent predictors of alpha diversity, extreme climate conditions such as maximum summer temperature and dry-season precipitation were most often associated with multivariate taxonomic and functional composition. Specifically, sites with high maximum temperatures and low dry-season precipitation housed communities containing high abundances of large predatory taxa. Furthermore, both climate dissimilarity and abiotic dissimilarity determined taxonomic turnover among sites (beta diversity). These findings suggest that while local-scale environmental variables may predict alpha diversity, climatic variability is important to consider when projecting broad-scale aquatic community responses to the extreme temperature and precipitation events that are expected for much of the world during the next century.},
-author = {Boersma, Kate S. and Nickerson, Avery and Francis, Clinton D. and Siepielski, Adam M.},
-doi = {10.1002/ece3.2517},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Boersma et al. - 2016 - Climate extremes are associated with invertebrate taxonomic and functional composition in mountain lakes.pdf:pdf},
-journal = {Ecology and Evolution},
-title = {{Climate extremes are associated with invertebrate taxonomic and functional composition in mountain lakes}},
-url = {http://doi.wiley.com/10.1002/ece3.2517},
-volume = {in press},
-year = {2016}
-}
-@article{Winemiller2015,
-abstract = {Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.},
-author = {Winemiller, Kirk O. and Fitzgerald, Daniel B. and Bower, Luke M. and Pianka, Eric R.},
-doi = {10.1111/ele.12462},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Winemiller et al. - 2015 - Functional traits, convergent evolution, and periodic tables of niches.pdf:pdf},
-journal = {Ecology Letters},
-number = {8},
-pages = {737--751},
-pmid = {26096695},
-title = {{Functional traits, convergent evolution, and periodic tables of niches}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12462/abstract},
-volume = {18},
-year = {2015}
-}
-@book{Dagnelie1981,
-author = {Dagnelie, Pierre},
-publisher = {Les presses agronomiques de Gembloux},
-title = {{Principes d'exp{\'{e}}rimentation}},
-year = {1981}
-}
-@article{Herrera2008,
-abstract = {Both the fossil record and molecular data support a long evolutionary history for the Araceae. Although the family is diverse in tropical America today, most araceous fossils, however, have been recorded from middle and high latitudes. Here, we report fossil leaves of Araceae from the middle-late Paleocene of northern Colombia, and review fossil araceous pollen grains from the same interval. Two of the fossil leaf species are placed in the new fossil morphogenus Petrocardium Herrera, Jaramillo, Dilcher, Wing et Gomez-N gen. nov.; these fossils are very similar in leaf morphology to extant Anthurium; however, their relationship to the genus is still unresolved. A third fossil leaf type from Cerrej{\'{o}}n is recognized as a species of the extant genus Montrichardia, the first fossil record for this genus. These fossils inhabited a coastal rainforest ∼60-58 million years ago with broadly similar habitat preferences to modern Araceae.},
-author = {Herrera, Fabiany A. and Jaramillo, Carlos A. and Dilcher, David L. and Wing, Scott L. and G{\'{o}}mez-N., Carolina},
-doi = {10.3732/ajb.0800172},
-journal = {American Journal of Botany},
-number = {12},
-pages = {1569--1583},
-title = {{Fossil araceae from a paleocene neotropical rainforest in Colombia}},
-volume = {95},
-year = {2008}
-}
-@article{Wallace1854,
-abstract = {Wallace, A. R. 1852. On the monkeys of the Amazon. Proceedings of the Zoological Society of London 20:107–110.},
-author = {Wallace, Alfred R},
-doi = {10.1080/037454809494374},
-isbn = {0022293140},
-issn = {0374-5481},
-journal = {Journal of Natural History},
-number = {14:84},
-pages = {451--454},
-title = {{On the Monkeys of the Amazon}},
-volume = {Series 2},
-year = {1854}
-}
-@article{McCoy2013,
-abstract = {In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply count-only measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, but are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different data sets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPD{\_}$\backslash$theta, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. In all three of the datasets considered, an abundance-weighted measure is the best differentiator between community states. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.},
-author = {McCoy, Connor O and Matsen, Frederick A},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/McCoy, Matsen - 2013 - Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampl.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth}},
-url = {http://arxiv.org/abs/1305.0306v1},
-volume = {1305.0306},
-year = {2013}
-}
-@article{Tokeshi1993,
-abstract = {Despite the fact that a substantial research effort has been directed at the analysis of species abundance patterns over the years, there are many important issues which are not sufficiently explored and understood. This review examines the conceptual and methodological frameworks of analysis in species abundance patterns, with particular emphasis on interpreting patterns in the context of community structure and organization.},
-author = {Tokeshi, Mutsunori},
-doi = {10.1016/S0065-2504(08)60042-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Tokeshi - 1993 - Species Abundance Patterns and Community Structure.pdf:pdf},
-journal = {Advances in Ecological Research},
-pages = {111--186},
-title = {{Species Abundance Patterns and Community Structure}},
-url = {http://www.sciencedirect.com/science/article/pii/S0065250408600422},
-volume = {24},
-year = {1993}
-}
-@article{Chao2010,
-abstract = {We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.},
-annote = {Times Cited: 0},
-author = {Chao, Anne and Chiu, Chun-Huo and Jost, Lou},
-doi = {10.1098/rstb.2010.0272 Supplementary},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Chiu, Jost - 2010 - Phylogenetic diversity measures based on Hill numbers.pdf:pdf},
-journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
-number = {1558},
-pages = {3599--3609},
-title = {{Phylogenetic diversity measures based on Hill numbers}},
-url = {http://rstb.royalsocietypublishing.org/content/suppl/2010/10/09/365.1558.3599.DC1.html},
-volume = {365},
-year = {2010}
-}
-@article{Harms2001,
-abstract = {1 Tests of habitat association among species of tropical trees and shrubs often assume that individual stems can be treated as independent sample units, even though limited dispersal conflicts with this assumption by causing new recruits to occur near maternal parents and siblings. 2 We developed methods for assessing patterns of association between mapped plants and mapped habitat types that explicitly incorporate spatial structure, thereby eliminating the need to assume independence among stems. 3 We used these methods to determine habitat-association patterns for 171 species of trees and shrubs within the permanent 50-ha Forest Dynamics Project plot on Barro Colorado Island, Panama. 4 Many fewer significant habitat associations result from the new methods than from traditional, but inappropriate, chi-square tests. The low-lying plateau, the most extensive habitat on the 50-ha plot, had nine species positively associated with it and 19 species negatively associated, leaving 143 species whose distributions were not biased with respect to this habitat. A small swamp in the plot was the most distinct habitat, with 32 species positively and 20 species negatively associated, leaving more than two-thirds of the species neither positively nor negatively associated. 5 To the extent that habitat association reflects habitat specialization, our results suggest that local habitat specialization plays a limited role in the maintenance of species diversity in this forest},
-author = {Harms, Kyle E. and Condit, Richard and Hubbell, Stephen P. and Foster, Robin B.},
-doi = {10.1111/j.1365-2745.2001.00615.x/full},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Harms et al. - 2001 - Habitat association of trees and shrubs in a 50-ha neotropical forest plot.pdf:pdf},
-journal = {Journal of Ecology},
-number = {6},
-pages = {947--959},
-title = {{Habitat association of trees and shrubs in a 50-ha neotropical forest plot}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2001.00615.x/full},
-volume = {89},
-year = {2001}
-}
-@article{Beguin1979a,
-abstract = {Geographical space is a major concept in spatial analysis. Curiously enough, no attempt has so far been made to provide a general and rigorous presentation. In this paper, a formal definition of the basic geographical components is given. For that purpose, topology and measure theory are used. A general definition of geographical space is then proposed and some properties are examined. Finally, the relations between the proposed definition and the particular representations used in spatial analysis are discussed.},
-author = {Beguin, Hubert and Thisse, Jacques-Fran{\c{c}}ois},
-doi = {10.1111/j.1538-4632.1979.tb00700.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Beguin, Thisse - 1979 - An axiomatic Approach to Geographical Space.pdf:pdf},
-journal = {Geographical Analysis},
-number = {4},
-pages = {325--341},
-title = {{An axiomatic Approach to Geographical Space}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1538-4632.1979.tb00700.x/full},
-volume = {11},
-year = {1979}
-}
-@article{Aubreville1938,
-author = {Aubr{\'{e}}ville, A.},
-journal = {Scientia},
-number = {63},
-pages = {157},
-title = {{La for{\^{e}}t {\'{e}}quatoriale et les formations foresti{\`{e}}res tropicales africaines}},
-volume = {32},
-year = {1938}
-}
-@article{Devereux2004,
-abstract = {We investigate the geographic concentration and agglomeration of production activity in the UK at the four-digit industry level using a variety of measures. We relate these to comparable patterns in the US and France and find several similarities. We find that conditioning on industrial concentration, the most geographically concentrated industries appear to be relatively low-tech. We find evidence that plant survival rates are higher and both entry and exit rates are lower in more agglomerated industries, but that in some of the most agglomerated industries entry acts to re-enforce agglomeration.},
-author = {Devereux, Michael P. and Griffith, Rachel and Simpson, Helen},
-doi = {10.1016/S0166-0462(03)00073-5},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Devereux, Griffith, Simpson - 2004 - The Geographic Distribution of Production Activity in the UK.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-number = {5},
-pages = {533--564},
-title = {{The Geographic Distribution of Production Activity in the UK}},
-url = {http://www.sciencedirect.com/science/article/B6V89-49FR9K8-1/2/06b7b06bfecdac63c9be80ca10f2f5ed},
-volume = {34},
-year = {2004}
-}
-@article{Sakai2016,
-abstract = {Many axiomatic definitions of entropy, such as the R$\backslash$'enyi entropy, of a random variable are closely related to the {\$}\backslashell{\_}{\{}\backslashalpha{\}}{\$}-norm of its probability distribution. This study considers probability distributions on finite sets, and examines the sharp bounds of the {\$}\backslashell{\_}{\{}\backslashbeta{\}}{\$}-norm with a fixed {\$}\backslashell{\_}{\{}\backslashalpha{\}}{\$}-norm, {\$}\backslashalpha \backslashneq \backslashbeta{\$}, for {\$}n{\$}-dimensional probability vectors with an integer {\$}n \backslashge 2{\$}. From the results, we derive the sharp bounds of the R$\backslash$'enyi entropy of positive order {\$}\backslashbeta{\$} with a fixed R$\backslash$'enyi entropy of another positive order {\$}\backslashalpha{\$}. As applications, we investigate sharp bounds of Ariomoto's mutual information of order {\$}\backslashalpha{\$} and Gallager's random coding exponents for uniformly focusing channels under the uniform input distribution.},
-archivePrefix = {arXiv},
-arxivId = {1605.00019},
-author = {Sakai, Yuta and Iwata, Ken-ichi},
-eprint = {1605.00019},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Sakai, Iwata - 2016 - Sharp Bounds Between Two R{\'{e}}nyi Entropies of Distinct Positive Orders.pdf:pdf},
-journal = {arXiv},
-number = {v2},
-title = {{Sharp Bounds Between Two R{\'{e}}nyi Entropies of Distinct Positive Orders}},
-url = {http://arxiv.org/abs/1605.00019},
-volume = {1605.00019},
-year = {2016}
-}
-@article{Louf2015,
-abstract = {The spatial distribution of income shapes the structure and organisation of cities and its understanding has broad societal implications. Despite an abundant literature, many issues remain however unclear: there is no clear definition of what segregation is, no unambiguous definition of income classes, no clear way to identify neighborhoods, and no method to deal with the polycentric organization of large cities. In this paper, we address all these questions within a unique theoretical framework. We assume that households belonging to the same class tend to live close to each other, and households from different classes tend to avoid one another. Applied to the US 2000 Census Income data, 3 distinct classes emerge from the clustering of the original 16 income classes. Using these unambiguously defined classes, we cluster together contiguous similar areas and find that the number of clusters for each category scales with the city population, an effect that is more pronounced for rich households. Finally, using the density -- and not the distance to a center which is meaningless in polycentric cities -- we find that the richer class is overrepresented in high density zones, especially for larger cities. This suggests that density is a relevant factor for understanding the income structure of cities and might explain some of the differences observed between US and European cities.},
-archivePrefix = {arXiv},
-arxivId = {1511.04268},
-author = {Louf, R{\'{e}}mi and Barthelemy, Marc},
-doi = {10.1371/journal.pone.0157476},
-eprint = {1511.04268},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Louf, Barthelemy - 2016 - Patterns of Residential Segregation.PDF:PDF},
-journal = {PloS ONE},
-number = {6},
-pages = {e0157476},
-title = {{Patterns of Residential Segregation}},
-url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157476},
-volume = {11},
-year = {2016}
-}
-@article{Simpson1943,
-abstract = {There are three alternative fundamental hypotheses as to the nature of continents: that they are crustal segments permanent as entities but variable in position (drift hypothesis), that crustal positions do not vary significantly but continental segments and ocean basins do (transoceanic continents hypothesis), and that neither crustal positions nor the major distribution of continental and oceanic segments have varied greatly during at least the later stages of earth history (stable continents hypothesis). Biological data are important in choice between these hypotheses, but their compilation and treatment in the paleogeographical literature are usually inaccurate and often quite irresponsible. One part of this evidence, that derived from mammalian distribution, is here reviewed. The broader outlines of the past and present distribution of mammals on northern and on southern continents are separately examined, as far as they bear on choice between the three basic hypotheses. Examples of miscomprehension and misquotation are given. The evidence definitely opposes drifting or transoceanic continents and favors stable continents. Statements of intercontinental faunal resemblances are often misleading and their interpretations have usually been subjective, unreliable, and unscientific. A possible valid and more objective method is suggested and it is shown that preliminary study along these lines again favors stable continents. The history of a widely accepted but manifestly ill-founded transoceanic connection is sketched and the related theory of accordion continents is mentioned. Attempts to relate drift theories to the mammalian fauna of Madagascar are adversely criticized.},
-author = {Simpson, George Gaylord},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Simpson - 1943 - Mammals and the Nature of Continents.pdf:pdf},
-journal = {American Journal of Science},
-pages = {1--31},
-title = {{Mammals and the Nature of Continents}},
-url = {http://people.wku.edu/charles.smith/biogeog/SIMP943A.htm},
-volume = {241},
-year = {1943}
-}
-@article{Wardle2011,
-abstract = {Ecosystems worldwide are losing some species and gaining others, resulting in an interchange of species that is having profound impacts on how these ecosystems function. However, research on the effects of species gains and losses has developed largely independently of one another. Recent conceptual advances regarding effects of species gain have arisen from studies that have unraveled the mechanistic basis of how invading species with novel traits alter biotic interactions and ecosystem processes. In contrast, studies on traits associated with species loss are fewer, and much remains unknown about how traits that predispose species to extinction affect ecological processes. Species gains and losses are both consequences and drivers of global change; thus, explicit integration of research on how both processes simultaneously affect ecosystem functioning is key to determining the response of the Earth system to current and future human activities.},
-author = {Wardle, David A. and Bardgett, Richard D. and Callaway, Ragan M. and {Van der Putten}, Wim H.},
-doi = {10.1126/science.1197479},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Wardle et al. - 2011 - Terrestrial ecosystem responses to species gains and losses.pdf:pdf},
-journal = {Science},
-number = {6035},
-pages = {1273--7},
-title = {{Terrestrial ecosystem responses to species gains and losses.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/21659595},
-volume = {332},
-year = {2011}
-}
-@article{Lasky2014,
-abstract = {Theory predicts shifts in the magnitude and direction of biodiversity effects on ecosystem function (BEF) over succession, but this theory remains largely untested. We studied the relationship between aboveground tree biomass dynamics ($\Delta$biomass) and multiple dimensions of biodiversity over 8-16 years in eight successional rainforests. We tested whether successional changes in diversity-$\Delta$biomass correlations reflect predictions of niche theories. Diversity-$\Delta$biomass correlations were positive early but weak later in succession, suggesting saturation of niche space with increasing diversity. Early in succession, phylogenetic diversity and functional diversity in two leaf traits exhibited the strongest positive correlations with $\Delta$biomass, indicating complementarity or positive selection effects. In mid-successional stands, high biodiversity was associated with greater mortality-driven biomass loss, i.e. negative selection effects, suggesting successional niche trade-offs and loss of fast-growing pioneer species. Our results demonstrate that BEF relationships are dynamic across succession, thus successional context is essential to understanding BEF in a given system.},
-author = {Lasky, Jesse R. and Uriarte, Mar{\'{i}}a and Boukili, Vanessa K. and Erickson, David L. and {John Kress}, W. and Chazdon, Robin L.},
-doi = {10.1111/ele.12322},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lasky et al. - 2014 - The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession.pdf:pdf},
-journal = {Ecology letters},
-number = {9},
-pages = {1158--1167},
-title = {{The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession.}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12322/abstract},
-volume = {17},
-year = {2014}
-}
-@article{May2015,
-abstract = {Assessing the relative importance of different processes that determine the spatial distribution of species and the dynamics in highly diverse plant communities remains a challenging question in ecology. Previous modelling approaches often focused on single aggregated forest diversity patterns that convey limited information on the underlying dynamic processes. Here, we use recent advances in inference for stochastic simulation models to evaluate the ability of a spatially explicit and spatially continuous neutral model to quantitatively predict six spatial and non-spatial patterns observed at the 50 ha tropical forest plot on Barro Colorado Island, Panama. The patterns capture different aspects of forest dynamics and biodiversity structure, such as annual mortality rate, species richness, species abundance distribution, beta-diversity and the species–area relationship (SAR). The model correctly predicted each pattern independently and up to five patterns simultaneously. However, the model was unable to match the SAR and beta-diversity simultaneously. Our study moves previous theory towards a dynamic spatial theory of biodiversity and demonstrates the value of spatial data to identify ecological processes. This opens up new avenues to evaluate the consequences of additional process for community assembly and dynamics.},
-author = {May, Felix and Huth, Andreas and Wiegand, Thorsten},
-doi = {10.1098/rspb.2014.1657},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/May, Huth, Wiegand - 2015 - Moving beyond abundance distributions neutral theory and spatial patterns in a tropical forest.pdf:pdf},
-journal = {Proceedings of the Royal Society of London, Series B: Biological Sciences},
-number = {1802},
-pages = {20141657},
-title = {{Moving beyond abundance distributions: neutral theory and spatial patterns in a tropical forest}},
-url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2014.1657},
-volume = {282},
-year = {2015}
-}
-@inproceedings{Moradi2016,
-abstract = {We consider an inhomogeneous point process on a linear network, and extend Diggle's nonparametric kernel-based edge-corrected intensity estimator in this context. We compare the accuracy and performance of Diggle's method with respect to the equal-split discontinuous kernel estimator. We show the improvement on the estimation of second-order summary statistics, in particular on the inhomogeneous geometrically corrected network K- and pair correlation functions. Finally, we analyse a spatial point pattern of calls related to anti-social behaviour in the streets of a Spanish town.},
-address = {Valencia. Spain},
-author = {Moradi, Mohammad Mehdi and Rodr{\'{i}}guez-Cort{\'{e}}s, F. J. and Mateu, Jorge},
-booktitle = {Proceedings of METMA VIII: 8th International workshop on spatio-temporal modelling},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Moradi, Rodr{\'{i}}guez-Cort{\'{e}}s, Mateu - 2016 - An adapted intensity estimator for linear networks with an application to modelling anti-social.pdf:pdf},
-pages = {121--124},
-title = {{An adapted intensity estimator for linear networks with an application to modelling anti-social behaviour in an urban environment}},
-year = {2016}
-}
-@article{Stoyan1984,
-author = {Stoyan, Dietrich and Ohser, J},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Stoyan, Ohser - 1984 - Cross-correlation measures for weighted random measures.pdf:pdf},
-journal = {Teoriya Veroyatnostei i ee Primeneniya},
-number = {2},
-pages = {338--347},
-title = {{Cross-correlation measures for weighted random measures}},
-volume = {29},
-year = {1984}
-}
-@article{Williams1994,
-abstract = {To assess conservation priorities, a means of measuring the distribution of a much larger part of overall bio- diversity is needed that will at the same time reduce the colossal sampling problems of exhaustive surveys. One possibility is a 'top-down' taxonomic approach, in which the biodiversity of different areas may be compared using measures based on the number of higher taxa present in each. The advantage of this approach is that survey costs should be greatly reduced because identification to species level, particularly within the few hyper-rich higher taxa, would be unnecessary. We report that family richness is a good predictor of species richness for a variety of groups and regions, including both British ferns and British butterflies among 100 km x 100 km (10,000 km 2) grid squares, Australian passerine birds among 5 ° x 5 ° grid squares (c. 220,000-310,000 km 2) and 10 ° x 10 ° grid squares (c. 970,000-1,190,000 km2), and North and Central American bats among grid squares of c. 611,000 km 2. With careful choice of higher-taxon rank, it may be possible to re-deploy effort from taxonomically intensive to taxonomically extensive surveys, in order to estimate the global distribution of a much larger proportion of overall biodiversity at the same cost.},
-author = {Williams, P. H. and Gaston, Kevin J.},
-doi = {10.1016/0006-3207(94)90612-2},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Williams, Gaston - 1994 - Measuring more of biodiversity can higher-taxon richness predict wholesale species richness.pdf:pdf},
-journal = {Biological Conservation},
-pages = {211--217},
-title = {{Measuring more of biodiversity: can higher-taxon richness predict wholesale species richness?}},
-url = {http://www.sciencedirect.com/science/article/pii/0006320794906122},
-volume = {67},
-year = {1994}
-}
-@article{Walker1992,
-abstract = {This paper addresses the problem of which biota to choose to best satisfy the conservation goals for a particular region in the face of inadequate resources, Biodiversity is taken to be the integration of biological variability across all scales, from the genetic, through species and ecosystems, to landscapes. Conserving biodiversity is a daunting task, and the paper asserts that focusing on species is not the best approach. The best way to minimize species loss is to maintain the integrity of ecosystem function. The important questions therefore concern the kinds of biodiversity that are significant to ecosystem functioning. To best focus our efforts we need to establish how much (or how little) redundancy there is in the biological composition of ecosystems. An approach is suggested, based on the use of functional groups of organisms defined according to ecosystem processes. Functional groups with little or no redundancy warrant priority conservation effort. Complementary species-based approaches for maximizing the inclusion of biodiversity within a set of conservation areas are compared to the functional-group approach.},
-author = {Walker, Brian H.},
-doi = {10.1046/j.1523-1739.1992.610018.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Walker - 1992 - Biodiversity and Ecological Redundancy.pdf:pdf},
-journal = {Conservation biology},
-number = {1},
-pages = {18--23},
-title = {{Biodiversity and Ecological Redundancy}},
-url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1523-1739.1992.610018.x/full},
-volume = {6},
-year = {1992}
-}
-@article{Roder1975,
-author = {Roder, Wolf},
-doi = {10.1111/j.0033-0124.1975.00432.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Roder - 1975 - A procedure for assessing point patterns without reference to area or density.pdf:pdf},
-journal = {The Professional Geographer},
-number = {4},
-pages = {432--440},
-title = {{A procedure for assessing point patterns without reference to area or density}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0033-0124.1975.00432.x/full},
-volume = {XXVII},
-year = {1975}
-}
-@article{Ellison2010,
-abstract = {Why do firms cluster near one another? We test Marshall's theories of industrial agglomeration by examining which industries locate near one another, or coagglomerate. We construct pairwise coagglomeration indices for US manufacturing industries from the Economic Census. We then relate coagglomeration levels to the degree to which industry pairs share goods, labor, or ideas. To reduce reverse causality, where collocation drives input-output linkages or hiring patterns, we use data from UK industries and from US areas where the two industries are not collocated. All three of Marshall's theories of agglomeration are supported, with input-output linkages particularly important.},
-author = {Ellison, Glenn and Glaeser, Edward L and Kerr, William R},
-doi = {10.1257/aer.100.3.1195},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ellison, Glaeser, Kerr - 2010 - What Causes Industry Agglomeration Evidence from Coagglomeration Patterns.pdf:pdf},
-journal = {The American Economic Review},
-number = {3},
-pages = {1195--1213},
-title = {{What Causes Industry Agglomeration? Evidence from Coagglomeration Patterns}},
-url = {https://www.aeaweb.org/articles?id=10.1257/aer.100.3.1195},
-volume = {100},
-year = {2010}
-}
-@article{Bonan1988,
-abstract = {The role of neighborhood competition in the formation of size hierarchies was investigated using an individual-plant, spatially explicit growth model of annual plant population dynamics. Neighborhood effects were vaned by having plants grow individually and in random and hexagonal spatial patterns. Resources shared between two individuals were allocated symmetrically or asymmetrically. The effect of genetic variability was controlled by first assigning constant initial masses and growth rate coefficients for all individuals and then drawing these parameters from normal frequency distributions. Size hierarchies formed when relative growth rates were positively correlated with plant mass. Neighborhood effects were an important means of inducing this relationship. When plants competed for resources, individuals had the same relative values of available growingspace, relative growth rate, and mass so that size differences were enhanced over time. However, genetic variation in growth rates also caused a positive correlation between plant mass and relative growth rate. In this case, regardless of the type of resource allocation, neighborhood competition increased the variability in growth rates beyond that expected from genetic variation. These theoretical results suggest the importance of neighborhood effects in the formation of size hierarchies and imply that size structure is in part an expression of the spatial distribution and availability of resources within a stand.},
-author = {Bonan, Gordon B.},
-doi = {10.2307/1941150},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bonan - 1988 - The Size Structure of Theoretical Plant Populations Spatial Patterns and Neighborhood Effects.pdf:pdf},
-journal = {Ecology},
-number = {6},
-pages = {1721--1730},
-title = {{The Size Structure of Theoretical Plant Populations: Spatial Patterns and Neighborhood Effects}},
-url = {http://onlinelibrary.wiley.com/doi/10.2307/1941150/abstract},
-volume = {69},
-year = {1988}
-}
-@article{Day2003,
-abstract = {1 Early in growth, plant populations subjected to heterogeneous conditions can achieve significantly higher yields than populations grown in homogeneous conditions that provide the same amount of nutrients. We hypothesized that this yield enhancement would be ephemeral, and that yields of populations grown under different patterns of nutrient supply will converge as time passes. We also predicted that plant size frequency distributions will continue to differ between populations in heterogeneous and homogeneous conditions, that spatial patterns of mortality will differ, and that greater mortality will occur in populations under heterogeneous conditions. An experiment was carried out on Cardamine hirsuta to test these hypotheses. 2 The experiment was harvested after 60 days, when flowering had begun in all populations. At this time, populations grown with the same nutrient supply but different patterns of supply did not differ in yield. Populations grown at higher nutrient levels had greater yields but suffered more mortality. 3 In heterogeneous conditions, plants in nutrient-rich locations were larger than plants in nutrient-poor locations, and larger than plants in identical positions in populations growing under homogeneous conditions. Plants in nutrient-rich patches in heterogeneous treatments suffered more mortality than plants in nutrient-poor patches. Contrary to prediction, total mortality at all levels of nutrient supply was significantly higher in populations in homogeneous conditions. 4 Coefficient of variation in shoot sizes was higher in populations at higher nutrient levels, but unaffected by pattern of nutrient supply. CV of root mass per unit of substrate was greater under heterogeneous than homogeneous conditions. 5 Frequency distributions of shoot size, and root mass per unit of substrate, were strikingly different between populations grown under different patterns of nutrient supply. The differences are interpreted as showing that under homogeneous conditions all parts of the habitat are heavily exploited, giving rise to uniformly high levels of interplant competition. In contrast, nutrient-poor patches in the heterogeneous treatments contain low root masses. Plants in these patches remain small, but have a high probability of survival. We propose that these differences in intensity of habitat occupation, and presumably in competition, explain the lower mortality in populations growing under heterogeneous conditions.},
-author = {Day, Kieron J. and Hutchings, Michael J. and John, Elizabeth A.},
-doi = {10.1046/j.1365-2745.2003.00799.x/abs},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Day, Hutchings, John - 2003 - The effects of spatial pattern of nutrient supply on yield, structure and mortality in plant populations.pdf:pdf},
-journal = {Journal of Ecology},
-number = {4},
-pages = {541--553},
-title = {{The effects of spatial pattern of nutrient supply on yield, structure and mortality in plant populations}},
-url = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2745.2003.00799.x/abs},
-volume = {91},
-year = {2003}
-}
-@article{Finegan2015,
-abstract = {1. Tropical forests are globally important, but it is not clear whether biodiversity enhances carbon storage and sequestration in them. We tested this relationship focusing on components of functional trait biodiversity as predictors. 2. Data are presented for three rain forests in Bolivia, Brazil and Costa Rica. Initial above-ground biomass and biomass increments of survivors, recruits and survivors + recruits (total) were estimated for trees ≥10 cm d.b.h. in 62 and 21 1.0-ha plots, respectively. We determined relationships of bio-mass increments to initial standing biomass (AGB i), biomass-weighted community mean values (CWM) of eight functional traits and four functional trait variety indices (functional richness, func-tional evenness, functional diversity and functional dispersion). 3. The forest continuum sampled ranged from 'slow' stands dominated by trees with tough tissues and high AGB i , to 'fast' stands dominated by trees with soft, nutrient-rich leaves, lighter woods and lower AGB i . 4. We tested whether AGB i and biomass increments were related to the CWM trait values of the dominant species in the system (the biomass ratio hypothesis), to the variety of functional trait val-ues (the niche complementarity hypothesis), or in the case of biomass increments, simply to initial standing biomass (the green soup hypothesis). 5. CWMs were reasonable bivariate predictors of AGB i and biomass increments, with CWM specific leaf area SLA, CWM leaf nitrogen content, CWM force to tear the leaf, CWM maximum adult height H max and CWM wood specific gravity the most important. AGB i was also a reasonable predictor of the three measures of biomass increment. In best-fit multiple regression models, CWM H max was the most important predictor of initial standing biomass AGB i . Only leaf traits were selected in the best models for biomass increment; CWM SLA was the most important predictor, with the expected posi-tive relationship. There were no relationships of functional variety indices to biomass increments, and AGB i was the only predictor for biomass increments from recruits. 6. Synthesis. We found no support for the niche complementarity hypothesis and support for the green soup hypothesis only for biomass increments of recruits. We have strong support for the biomass ratio hypothesis. CWM H max is a strong driver of ecosystem biomass and carbon storage and CWM SLA, and other CWM leaf traits are especially important for biomass increments and carbon sequestration.},
-author = {Finegan, Bryan and Pe{\~{n}}a-Claros, Marielos and de Oliveira, Alexandre and Ascarrunz, Nataly and Bret-Harte, M. Syndonia and Carre{\~{n}}o-Rocabado, Geovana and Casanoves, Fernando and D{\'{i}}az, Sandra and {Eguiguren Velepucha}, Paul and Fernandez, Fernando and Licona, Juan Carlos and Lorenzo, Leda and {Salgado Negret}, Beatriz and Vaz, Marcel and Poorter, Lourens},
-doi = {10.1111/1365-2745.12346},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Finegan et al. - 2015 - Does functional trait diversity predict above-ground biomass and productivity of tropical forests Testing three.pdf:pdf},
-journal = {Journal of Ecology},
-number = {1},
-pages = {191--201},
-title = {{Does functional trait diversity predict above-ground biomass and productivity of tropical forests? Testing three alternative hypotheses}},
-volume = {103},
-year = {2015}
-}
-@incollection{Gibbons2014,
-abstract = {This chapter is concerned with methods for analysing spatial data. After initial discussion on the nature of spatial data, including the concept of randomness, we focus most of our attention on linear regression models that involve interactions between agents across space. The introduction of spatial variables in to standard linear re- gression provides a ‡exible way of characteristing these interactions, but complicates both interpretation and estimation of parameters of interest. The estimation of these models leads to three fundamental challenges: the ‘re‡ection problem', the presence of omitted variables and problems caused by sorting. We consider possible solutions to these problems, with a particular focus on restrictions on the nature of interactions. We show that similar assumptions are implicit in the empirical strategies - {\ldots}xed e¤ects or spatial di¤erencing - used to address these problems in reduced form estimation. These general lessons carry over to the policy evaluation literature.},
-address = {Amsterdam},
-author = {Gibbons, Steve and Overman, Henry G and Patacchini, Eleonora},
-booktitle = {Handbook of Regional {\&} Urban Economics},
-chapter = {3},
-editor = {Duranton, Gilles and Henderson, J Vernon and Strange, William C},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gibbons, Overman, Patacchini - 2014 - Spatial Methods.pdf:pdf},
-pages = {115--168},
-publisher = {Elsevier. North Holland},
-title = {{Spatial Methods}},
-volume = {5},
-year = {2015}
-}
-@article{Barthes1991,
-abstract = {An attempt is made to assess the relationships between soil conditions and the spatial distribution of two sympatric species of rain forest trees belonging to genus Eperua (Caesalpiniaceae). The study was carried out at the Paracou study site, French Guiana, on the domed bills of precambrian basement rock, locally schistose or migmatic. The relationships between the distribution of individuals of both species and soil variables (126 samples) were studied using factor analysis and hierarchical classification. Eperua falcata is mostly found on hydromorphic or shallow vertically drained soils, often with a high exchangeable aluminium content. This tree appears to be weil adapted to unfavourable soil conditions, but it can also be found in other situations. Eperua grandiflora is also adapted to shallow soils, but it does not withstand hydromorphic conditions as weil as E. falcata ; it is also very sensitive to the high aluminium content of the soil. The two Eperua species are therefore complementary to one another, except on shallow soils, thus allowing genus Eperua to fill different edaphic niches},
-author = {Barthes, Bernard},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Barthes - 1991 - Influence des caract{\`{e}}res p{\'{e}}dologiques sur la r{\'{e}}partition spatiale de deux esp{\`{e}}ces du genre Eperua (Caesalpiniaceae) en.pdf:pdf},
-journal = {Revue d'Ecologie (La Terre et la Vie)},
-number = {4},
-pages = {303--320},
-title = {{Influence des caract{\`{e}}res p{\'{e}}dologiques sur la r{\'{e}}partition spatiale de deux esp{\`{e}}ces du genre Eperua (Caesalpiniaceae) en for{\^{e}}t guyanaise}},
-url = {http://documents.irevues.inist.fr/handle/2042/54654},
-volume = {46},
-year = {1991}
-}
-@book{Greenacre2013,
-author = {Greenacre, Michael and Primicerio, Raul},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}1-Pr{\'{e}}face.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}2-Index.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}3-Auteur.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}appa.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}appb.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}appc.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch01.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch02.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch03.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch04.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch05.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch06.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch07.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch08.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch09.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch10.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch11.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch12.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch14.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch15.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch16.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch17.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch18.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch19.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}ch20.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}index.pdf:pdf;:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/greenacre{\_}maed{\_}list.pdf:pdf},
-isbn = {9788492937509},
-number = {December},
-publisher = {Fundaci{\'{o}}n BBVA},
-title = {{Multivariate Analysis of Ecological Data}},
-url = {http://www.fbbva.es/TLFU/tlfu/esp/publicaciones/libros/fichalibro/index.jsp?codigo=769},
-year = {2013}
-}
-@article{Butturi-Gomes2017,
-abstract = {The Pallmann-Scherer test is a promising multicomparison procedure to test statistical hypotheses regarding generalized diversity/entropy indices, such as Tsallis family and Hill numbers (SqSq and HqHq, respectively), which represent alternative ways of profiling species diversity along a gradient of emphasis on species richness versus evenness in abundance distributions. Given the pressing importance of reliably comparing diversity across ecological communities, and since only a few of such procedures are currently available, knowing its statistical performance under realistic ecological scenarios is of strategic importance. In this paper, we evaluated the performance of the Pallmann-Scherer test using computer simulations of communities following different species-abundance distributions, spatially aggregated as widely observed empirically, and sampled by a commonly used quadrat procedure. We found that the test is very conservative for both SqSq and HqHq, leading to biased significance levels, with low probabilities of type-I error but high probabilities of type-II error (i.e., low statistical power). Although it should be acknowledged that the current method represents an important starting point, further improvements must be made in order to enhance its power and meet the required standards in comparative studies of diversity.},
-author = {Butturi-Gomes, Davi and Petrere, Miguel and Giacomini, Henrique C. and Zocchi, Silvio Sandoval},
-doi = {10.1016/j.ecolind.2016.08.054},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Butturi-Gomes et al. - 2017 - Statistical performance of a multicomparison method for generalized species diversity indices under realis.pdf:pdf},
-journal = {Ecological Indicators},
-pages = {545--552},
-title = {{Statistical performance of a multicomparison method for generalized species diversity indices under realistic empirical scenarios}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S1470160X16305258},
-volume = {72},
-year = {2017}
-}
-@article{Elith2009,
-abstract = {Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.},
-author = {Elith, Jane and Leathwick, John R.},
-doi = {10.1146/annurev.ecolsys.110308.120159},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Elith, Leathwick - 2009 - Species Distribution Models Ecological Explanation and Prediction Across Space and Time(2).pdf:pdf},
-journal = {Annual Review of Ecology, Evolution, and Systematics},
-number = {1},
-pages = {677--697},
-title = {{Species Distribution Models: Ecological Explanation and Prediction Across Space and Time}},
-url = {http://www.annualreviews.org/doi/10.1146/annurev.ecolsys.110308.120159},
-volume = {40},
-year = {2009}
-}
-@article{Biondi1994,
-abstract = {La g{\'{e}}ostatistique fournit les outils pour mod{\'{e}}liser, estimer, cartographier et {\'{e}}ventuellement pr{\'{e}}dire la distribution spatiale des arbres selon leur diam{\`{e}}tre, leur surface terri{\`{e}}re et leur accroissement p{\'{e}}riodique. La variation temporelle de la corr{\'{e}}lation spatiale est {\'{e}}valu{\'{e}}e entre 1920 et 1990 par p{\'{e}}riode de 10 ans. Le peuplement {\'{e}}tudi{\'{e}} est une vieille futaie de Pinusponderosa Dougl. ex Laws, du sud-ouest des Etats-Unis issue de r{\'{e}}g{\'{e}}n{\'{e}}ration naturelle et dont la surface terri{\`{e}}re et la densit{\'{e}} ont augment{\'{e}} de fa{\c{c}}on soutenue au cours des derni{\`{e}}res d{\'{e}}cennies. L'objectif consiste {\`{a}} d{\'{e}}terminer si, tout en r{\'{e}}duisant l'accroissement des arbres individuels, l'augmentation de la densit{\'{e}} modifie aussi leur corr{\'{e}}lation spatiale. Le variogramme construit r{\'{e}}v{\`{e}}le que la structure spatiale de la futaie {\'{e}}tudi{\'{e}}e n'a pas chang{\'{e}} entre 1920 et 1990. Il r{\'{e}}v{\`{e}}le aussi le regroupement des arbres par bouquets dont le diam{\`{e}}tre moyen est de 30 m. Le diam{\`{e}}tre des bouquets demeurant constant dans le temps, l'augmentation de la densit{\'{e}} est donc caus{\'{e}}e par l'augmentation du nombre de paquets et non par l'augmentation de leur diam{\`{e}}tre. La corr{\'{e}}lation spatiale de la taille des arbres reste toujours sup{\'{e}}rieure {\`{a}} celle de leur accroissement. Elle diminue avec le temps, mais moins vite que celle de leur accroissement. La faible corr{\'{e}}lation spatiale de l'accroissement observ{\'{e}}e {\`{a}} la derni{\`{e}}re d{\'{e}}cennie montre que l'accroissement varie ind{\'{e}}pendamment de la localisation des arbres dans le bouquet. L'augmentation de la densit{\'{e}} correspond non seulement {\`{a}} la diminution de la moyenne et de la variance de l'accroissement, mais aussi {\`{a}} la r{\'{e}}duction de sa corr{\'{e}}lation spatiale. Sachant que plus la densit{\'{e}} augmente, moins l'accroissement de l'abre individuel d{\'{e}}pend des distances avec ses voisins dans le bouquet, l'apport de la distribution spatiale des arbres dans la futaie {\`{a}} la pr{\'{e}}diction de leur accroissement devient nul lorsque la densit{\'{e}} d{\'{e}}passe un maximum critique. Les mod{\`{e}}les de simulation spatio-temporelle de la croissance des futaies peuvent {\^{e}}tre am{\'{e}}lior{\'{e}}s par l'int{\'{e}}gration des informations sur la corr{\'{e}}lation spatiale en faisant appel {\`{a}} la g{\'{e}}ostatistique.},
-author = {Biondi, Franco and Myers, Donald E. and Avery, Charles C.},
-doi = {10.1139/x94-176#.WBJUsCQiW9Y},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Biondi, Myers, Avery - 1994 - Geostatistically modelling stem size and increment in an old-growth forest.pdf:pdf},
-journal = {Canadian Journal of Forest Research},
-pages = {1354--1368},
-title = {{Geostatistically modelling stem size and increment in an old-growth forest}},
-url = {http://www.nrcresearchpress.com/doi/abs/10.1139/x94-176{\#}.WBJUsCQiW9Y},
-volume = {24},
-year = {1994}
-}
-@article{Feser2002,
-abstract = {We argue that cluster analysis is best viewed as a general mode of inquiry rather than a narrow technical methodology in regional economic analysis. The perspective emphasizes the value of cluster studies as starting points for open discussions among public officials, business leaders, and the lay public about their values and priorities for economic development. We illustrate our thesis with reference to two cluster studies that are influencing technology-focused regional development and education policy in the State of North Carolina.},
-author = {Feser, Edward J. and Luger, M. I.},
-doi = {10.1080/09654310303664},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Feser, Luger - 2002 - Cluster analysis as a mode of inquiry Its use in science and technology policymaking in North Carolina.pdf:pdf},
-journal = {European Planning Studies},
-number = {1},
-pages = {11--24},
-title = {{Cluster analysis as a mode of inquiry: Its use in science and technology policymaking in North Carolina}},
-url = {http://www.tandfonline.com/doi/abs/10.1080/09654310303664},
-volume = {11},
-year = {2002}
-}
-@book{Diggle1983,
-address = {London},
-author = {Diggle, Peter J.},
-pages = {1--148},
-publisher = {Academic Press},
-title = {{Statistical analysis of spatial point patterns}},
-year = {1983}
-}
-@article{Greenhut1959,
-author = {Greenhut, Melvin L.},
-doi = {10.2307/1927273},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Greenhut - 1959 - An Empirical Model and a Survey New Plant Locations in Florida.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {4},
-pages = {433--438},
-title = {{An Empirical Model and a Survey: New Plant Locations in Florida}},
-url = {https://www.jstor.org/stable/1927273},
-volume = {41},
-year = {1959}
-}
-@article{Cavender-Bares2009,
-abstract = {The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change. {\textcopyright} 2009 Blackwell Publishing Ltd/CNRS.},
-annote = {Cited By (since 1996): 112
-Export Date: 27 December 2011
-Source: Scopus
-CODEN: ECLEF
-doi: 10.1111/j.1461-0248.2009.01314.x
-PubMed ID: 19473217
-Language of Original Document: English
-Correspondence Address: Cavender-Bares, J.; Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, United States; email: cavender@umn.edu},
-author = {Cavender-Bares, Jeannine and Kozak, Kenneth H. and Fine, Paul V. A. and Kembel, Stephen W.},
-doi = {10.1111/j.1461-0248.2009.01314.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cavender-Bares et al. - 2009 - The merging of community ecology and phylogenetic biology.pdf:pdf},
-journal = {Ecology Letters},
-number = {7},
-pages = {693--715},
-title = {{The merging of community ecology and phylogenetic biology}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01314.x/abstract},
-volume = {12},
-year = {2009}
-}
-@article{Hoover1936,
-author = {Hoover, Edgar M.},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Hoover - 1936 - The Measurement of Industrial Localization.pdf:pdf},
-journal = {The Review of Economics and Statistics},
-number = {4},
-pages = {162--171},
-title = {{The Measurement of Industrial Localization}},
-volume = {18},
-year = {1936}
-}
-@article{Ledo2011,
-abstract = {The spatial pattern of the different species in complex ecosystems reflects the underlying ecological processes. In this paper a second order moment function is proposed and tested to analyse the spatial distribution of a mark, which could be a tree characteristic such as diameter or height, between two different types of points, which could be two different tree species. The proposed function was a conditional density function based on the intertype Krs(d) function, incorporating as test function the correlation of the marks between pairs composed of points of different types. The results obtained in simulated and real plots prove that the function is capable of revealing the scale at which spatial correlation of the mark between two types of points exists. The proposed function allows the spatial association between individuals of different species at different life stages to be identified. This analysis may reveal information on species ecology and interspecific interactions in forest ecosystems.},
-author = {Ledo, Alicia and Cond{\'{e}}s, Sonia and Montes, Fernando},
-doi = {10.1016/j.ecolmodel.2010.10.029},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Ledo, Cond{\'{e}}s, Montes - 2011 - Intertype mark correlation function A new tool for the analysis of species interactions.pdf:pdf},
-journal = {Ecological Modelling},
-number = {3},
-pages = {580--587},
-title = {{Intertype mark correlation function: A new tool for the analysis of species interactions}},
-url = {http://www.sciencedirect.com/science/article/pii/S0304380010005958},
-volume = {222},
-year = {2011}
-}
-@article{Watt1947,
-author = {Watt, Alex S.},
-doi = {10.2307/2256497},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Watt - 1947 - Pattern and process in the plant community.pdf:pdf},
-journal = {Journal of Ecology},
-pages = {1--22},
-title = {{Pattern and process in the plant community}},
-url = {https://www.jstor.org/stable/2256497},
-volume = {35},
-year = {1947}
-}
-@article{Cerquetti2014,
-abstract = {Tsallis entropy is a generalization of Shannon entropy first derived in Patil and Taillie (1982) and then rediscovered in community ecology by Keylock (2005) as a concave diversity measure addressing the self-similar and multifractal nature of the distribution and abundance of species. Bayesian nonparametric estimation of Shannon's and Simpson's diversity indices has been already advocated as an alternative to maximum likelihood estimation based on frequency counts, which is severely biased in the undersampled regime. Here we present a Bayesian nonparametric solution to Patil-Taillie-Tsallis diversity estimation under Gnedin-Pitman priors, a large class of random discrete distributions recently deeply investigated in posterior predictive species richness and discovery probability estimation. We provide closed form expressions for the first three moments of the posterior distribution and a general technique to obtain higher order moments.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1404.3441v1},
-author = {Cerquetti, Annalisa},
-eprint = {arXiv:1404.3441v1},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Cerquetti - 2014 - Bayesian nonparametric estimation of Patil-Taillie-Tsallis diversity under Gnedin–Pitman priors.pdf:pdf},
-journal = {arXiv},
-number = {v1},
-title = {{Bayesian nonparametric estimation of Patil-Taillie-Tsallis diversity under Gnedin–Pitman priors}},
-volume = {1404.3441},
-year = {2014}
-}
-@book{Pielou1977,
-address = {New York},
-author = {Pielou, Evelyn C.},
-publisher = {Wiley},
-title = {{Mathematical Ecology}},
-year = {1977}
-}
-@article{Chao2012,
-abstract = {A number of species richness estimators have been developed under the model that individuals (or sampling units) are sampled with replacement. However, if sampling is done without replacement so that no sampled unit can be repeatedly observed, then the traditional estimators for sampling with replacement tend to overestimate richness for relatively high-sampling fractions (ratio of sample size to the total number of sampling units) and do not converge to the true species richness when the sampling fraction approaches one. Based on abundance data or replicated incidence data, we propose a nonparametric lower bound for species richness in a single community and also a lower bound for the number of species shared by multiple communities. Our proposed lower bounds are derived under very general sampling models. They are universally valid for all types of species abundance distributions and species detection probabilities. For abundance data, individuals detectabilities are allowed to be heterogeneous among species. For replicated incidence data, the selected sampling units (e.g., quadrats) need not be fully censused and species can be spatially aggregated. All bounds converge correctly to the true parameters when the sampling fraction approaches one. Real data sets are used for illustration. We also test the proposed bounds by using subsamples generated from large real surveys or censuses, and their performance is compared with that of some previous estimators.},
-annote = {ISI Document Delivery No.: 011RW
-Times Cited: 0
-Cited Reference Count: 23
-Chao, Anne Lin, Chih-Wei
-Taiwan National Science Council
-The authors thank the Editor (Tom Louis), an Associate Editor and two reviewers for carefully reading an earlier version and providing insightful and thoughtful suggestions and comments, which substantially improved the paper. Especially, the reviewers' comments inspired us to develop very general sampling models. The development has greatly broadened the scope of our methods. We also sincerely thank Lou Jost and Bruno Walther for editing and offering very helpful comments. This work was supported by the Taiwan National Science Council.
-Wiley-blackwell
-Hoboken},
-author = {Chao, Anne and Lin, Chih-Wei},
-doi = {10.1111/j.1541-0420.2011.01739.x},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chao, Lin - 2012 - Nonparametric Lower Bounds for Species Richness and Shared Species Richness under Sampling without Replacement.pdf:pdf},
-journal = {Biometrics},
-number = {3},
-pages = {912--921},
-title = {{Nonparametric Lower Bounds for Species Richness and Shared Species Richness under Sampling without Replacement}},
-volume = {68},
-year = {2012}
-}
-@article{Kader2007,
-abstract = {Introductory statistics textbooks rarely discuss the concept of variability for a categorical variable and thus, in this case, do not provide a measure of variability. The impression is thus given that there is no measurement of variability for a categorical variable. A measure of variability depends on the concept of variability. Research has shown that "unalikeability" is a more natural concept than "variation about the mean" for many students. A "coefficient of unalikeablity" can be used to measure this type of variability. Variability in categorical data is different from variability in quantitative data. This paper develops the coefficient of unalikeability as a measure of categorical variability.},
-author = {Kader, Gary D. and Perry, Mike},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Kader, Perry - 2007 - Variability for Categorical Variables.pdf:pdf},
-journal = {Journal of Statistics Education},
-number = {2},
-title = {{Variability for Categorical Variables}},
-url = {http://www.amstat.org/publications/JSE/v15n2/kader.pdf},
-volume = {15},
-year = {2007}
-}
-@article{Marcon2012c,
-abstract = {Over the last decade, distance-based methods have been introduced and then improved in the field of spatial economics to gauge the geographic concentration of activities. There is a growing literature on this theme including new tools, discussions on their specific properties and various applications. However, there is currently no typology of distance-based methods. This paper fills that gap. The proposed classification helps understand all the properties of distance-based methods and proves that they are variations on the same framework.},
-author = {Marcon, Eric and Puech, Florence},
-doi = {10.1016/j.regsciurbeco.2016.10.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, Puech - 2017 - A Typology of Distance-Based Measures of Spatial Concentration.pdf:pdf},
-journal = {Regional Science and Urban Economics},
-pages = {56--67},
-title = {{A Typology of Distance-Based Measures of Spatial Concentration}},
-url = {http://www.sciencedirect.com/science/article/pii/S0166046216302782},
-volume = {62},
-year = {2017}
-}
-@article{Peterson1995,
-abstract = {1 The change in spatial pattern due to mortality over a period of 10 years was examined in a c. 60-year-old second-growth aspen-white-pine forest in northern Michigan, USA. 2 It is predicted that unitary plants undergoing competitive thinning will shift toward a more regular distribution of stems. Such a pattern has been reported for temperate jack pine (Pinus banksiana) and four tropical tree species, but was not seen in our population of canopy aspen. The distribution of aspen living in 1989 tended toward greater clumping than that expected from random mortality of aspen living in 1979. It is suggested that this contrast to theoretical predictions was due to the clonal nature of aspen. 3 White pine invading under aspen was clumped at all scales, both in 1979 and 1989, and its distribution showed significant repulsion from aspen at scales of 11 m and 14 m in 1989. This suggests that the net effect of the initially dominant aspen on invading white pine was one of inhibition of establishment, and that the spatial location and therefore the abundance of white pine was constrained by the locations of aspen ramets.},
-author = {Peterson, Chris J. and Squiers, Edwin R.},
-doi = {10.2307/2261421},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Peterson, Squiers - 1995 - An Unexpected Change in Spatial Pattern Across 10 Years in an Aspen-White Pine Forest.pdf:pdf},
-journal = {Journal of Ecology},
-number = {5},
-pages = {847--855},
-title = {{An Unexpected Change in Spatial Pattern Across 10 Years in an Aspen-White Pine Forest}},
-url = {https://www.jstor.org/stable/2261421},
-volume = {83},
-year = {1995}
-}
-@book{Mayr1942,
-address = {New York},
-author = {Mayr, Ernst},
-isbn = {0-674-86250-3},
-publisher = {Columbia University Press},
-title = {{Systematics and the origin of species from the viewpoint of a zoologist}},
-year = {1942}
-}
-@article{Bernstein1988a,
-abstract = {This paper presents estimates of the effects of intra- and interindustry R{\&}D investment spillovers on the costs and structure of production. The social rates of return to R{\&}D investment and their deviation from the private rate are also estimated. This is the first time that the consequences of R{\&}D spillovers are evaluated for Canadian industries. Intra- and interindustry spillovers decrease unit costs of production. Moreover, interindustry effects are substantially more elastic. Generally a firm's own R{\&}D capital is a substitute for R{\&}D capital obtained freely via spillovers. However, for firms operating in industries with relatively larger R{\&}D propensities, their own R{\&}D capital and the intra-industry spillover are complementary. In all industries the social rate of return greatly exceeds the private return, and the contribution of the interindustry spillover to the social return is virtually the same and small for all industries. Thus differentials between social and private returns and between social returns across industries depend on the extent of the intra-industry spillovers.},
-author = {Bernstein, Jeffrey I.},
-doi = {10.2307/135304},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Bernstein - 1988 - Costs of Production, Intra- and Interindustry R{\&}D Spillovers Canadian Evidence.pdf:pdf},
-journal = {The Canadian Journal of Economics},
-number = {2},
-pages = {324--347},
-title = {{Costs of Production, Intra- and Interindustry R{\&}D Spillovers: Canadian Evidence}},
-url = {https://www.jstor.org/stable/135304},
-volume = {21},
-year = {1988}
-}
-@book{Ternisien1997,
-address = {Trinit{\'{e}}, Martinique},
-author = {Ternisien, Aline and {Le Bellec}, Fabrice},
-pages = {1--504},
-publisher = {Gondwana Editions, Editions Orphie},
-title = {{Mon jardin tropical}},
-year = {1997}
-}
-@article{Miyadokoro2003,
-abstract = {We investigated the population structure and spatial pattern of major trees in a subalpine old-growth coniferous forest stand in the Ontake Forest Reserve of central Japan to examine the coexistence strategies of different species. We mapped all stems greater than or equal to5 cm in diameter at breast height (dbh) on a 2 ha plot. The stand contained nine woody plant species and 1508 living stems with a combined basal area of 55.6 m(2) ha(-1). The four major species were divided into two groups based on density and size/age structure. Group A (Abies mariesii and Abies veitchii) had a lower maximum age and higher density than group B, as well as reverse J- or L-shaped dbh distribution of live stems. Species in group B (Picea jezoensis var. hondoensis and Tsuga diversifolia) had very few stems in the understory, higher maximum ages than group A, and bell-shaped dbh distributions. Group B species may compensate for having fewer stems in the understory by having a longer lifespan, while species in group A may compensate for lower longevity by having numerous young stems in the understory. Canopy and understory stems of the four major coniferous species were patchily distributed throughout the plot. The distribution of canopy stems of species in group B was negatively associated with that of group A, but positively associated with understory stems in their own group. Similarly, the distribution of canopy stems of species in group A was negatively associated with that of understory stems of group B species. These results suggest species differences in favourable canopy and forest floor condition. Differences in life history strategies and site preferences may explain the coexistence of these species. (C) 2003 Elsevier Science B.V. All rights reserved.},
-author = {Miyadokoro, T and Nishimura, N and Yamamoto, S},
-doi = {10.1016/S0378-1127(03)00045-8},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Miyadokoro, Nishimura, Yamamoto - 2003 - Population structure and spatial patterns of major trees in a subalpine old-growth coniferous f.pdf:pdf},
-journal = {Forest Ecology and Management},
-number = {1-3},
-pages = {259--272},
-title = {{Population structure and spatial patterns of major trees in a subalpine old-growth coniferous forest, central Japan}},
-url = {http://www.sciencedirect.com/science/article/pii/S0378112703000458},
-volume = {182},
-year = {2003}
-}
-@book{StehliF.G.Webb1985,
-author = {{Stehli, F. G., Webb}, S. D.},
-publisher = {Plenium Press, New York},
-title = {{The Great American Biotic Interchange}},
-year = {1985}
-}
-@phdthesis{Sabatier1983,
-address = {Montpellier},
-author = {Sabatier, Daniel},
-publisher = {Universit{\'{e}} des Sciences et Techniques du Languedoc},
-title = {{Fructification et diss{\'{e}}mination en for{\^{e}}t guyanaise : l'exemple de quelques esp{\`{e}}ces ligneuses}},
-year = {1983}
-}
-@article{Gallopin2006,
-abstract = {This article uses a systemic perspective to identify and analyze the conceptual relations among vulnerability, resilience, and adaptive capacity within socio-ecological systems (SES). Since different intellectual traditions use the terms in different, sometimes incompatible, ways, they emerge as strongly related but unclear in the precise nature of their relationships. A set of diagnostic questions is proposed regarding the specification of the terms to develop a shared conceptual framework for the natural and social dimensions of global change. Also, development of a general theory of change in SESs is suggested as an important agenda item for research on global change.},
-author = {Gallop{\'{i}}n, Gilberto C.},
-doi = {10.1016/j.gloenvcha.2006.02.004},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Gallop{\'{i}}n - 2006 - Linkages between vulnerability, resilience, and adaptive capacity.pdf:pdf},
-journal = {Global Environmental Change},
-number = {3},
-pages = {293--303},
-title = {{Linkages between vulnerability, resilience, and adaptive capacity}},
-url = {http://www.sciencedirect.com/science/article/pii/S0959378006000409},
-volume = {16},
-year = {2006}
-}
-@book{croat1978flora,
-author = {Croat, T B},
-isbn = {9780804709507},
-publisher = {Stanford University Press},
-title = {{Flora of Barro Colorado Island}},
-url = {https://books.google.be/books?id=Whc{\_}ahfhFFoC},
-year = {1978}
-}
-@article{Kier9322,
-abstract = {Endemism and species richness are highly relevant to the global prioritization of conservation efforts in which oceanic islands have remained relatively neglected. When compared to mainland areas, oceanic islands in general are known for their high percentage of endemic species but only moderate levels of species richness, prompting the question of their relative conservation value. Here we quantify geographic patterns of endemism-scaled richness ({\{}$\backslash$textquotedblleft{\}}endemism richness{\{}$\backslash$textquotedblright{\}}) of vascular plants across 90 terrestrial biogeographic regions, including islands, worldwide and evaluate their congruence with terrestrial vertebrates. Endemism richness of plants and vertebrates is strongly related, and values on islands exceed those of mainland regions by a factor of 9.5 and 8.1 for plants and vertebrates, respectively. Comparisons of different measures of past and future human impact and land cover change further reveal marked differences between mainland and island regions. While island and mainland regions suffered equally from past habitat loss, we find the human impact index, a measure of current threat, to be significantly higher on islands. Projected land-cover changes for the year 2100 indicate that land-use-driven changes on islands might strongly increase in the future. Given their conservation risks, smaller land areas, and high levels of endemism richness, islands may offer particularly high returns for species conservation efforts and therefore warrant a high priority in global biodiversity conservation in this century.},
-author = {Kier, Gerold and Kreft, Holger and Lee, Tien Ming and Jetz, Walter and Ibisch, Pierre L and Nowicki, Christoph and Mutke, Jens and Barthlott, Wilhelm},
-doi = {10.1073/pnas.0810306106},
-issn = {0027-8424},
-journal = {Proceedings of the National Academy of Sciences},
-number = {23},
-pages = {9322--9327},
-publisher = {National Academy of Sciences},
-title = {{A global assessment of endemism and species richness across island and mainland regions}},
-url = {http://www.pnas.org/content/106/23/9322},
-volume = {106},
-year = {2009}
-}
-@article{Violle2017,
-abstract = {Rarity has been a central topic for conservation and evolutionary biologists aiming to determine the species characteristics that cause extinction risk. More recently, beyond the rarity of species, the rarity of functions or functional traits, called functional rarity, has gained momentum in helping to understand the impact of biodiversity decline on ecosystem functioning.However, a conceptual framework for defining and quantifying functional rarity is still lacking. We introduce 12 different forms of functional rarity along gradients of species scarcity and trait distinctiveness. We then highlight the potential key role of functional rarity in the long-term and large-scale maintenance of ecosystem processes, as well as the necessary linkage between functional and evolutionary rarity.},
-author = {Violle, Cyrille and Thuiller, Wilfried and Mouquet, Nicolas and Munoz, Fran{\c{c}}ois and Kraft, Nathan J. B. and Cadotte, Marc W. and Livingstone, Stuart W. and Mouillot, David},
-doi = {10.1016/j.tree.2017.02.002},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Violle et al. - 2017 - Functional Rarity The Ecology of Outliers.pdf:pdf},
-journal = {Trends in Ecology {\&} Evolution},
-title = {{Functional Rarity: The Ecology of Outliers}},
-url = {http://www.elsevier.com/artworkinstructions.},
-volume = {in press},
-year = {2017}
-}
-@book{comiskey1998forest,
-author = {Comiskey, J A and Dallmeier, F},
-isbn = {9781850709640},
-publisher = {Taylor {\&} Francis},
-series = {Forest Biodiversity in North, Central and South America, and the Caribbean: Research and Monitoring},
-title = {{Forest Biodiversity in North, Central and South America, and the Caribbean: Research and Monitoring}},
-url = {https://books.google.be/books?id=6KHX-HMtLGcC},
-year = {1998}
-}
-@article{Laurance2007c,
-abstract = {Tropical forests are the most biologically diverse and ecologically complex of terrestrial ecosystems, and are disappearing at alarming rates. It has long been suggested that rapid forest loss and degradation in the tropics, if unabated, could ultimately precipitate a wave of species extinctions, perhaps comparable to mass extinction events in the geological history of the Earth. However, a vigorous debate has erupted following a study by Wright and Muller-Landau that challenges the notion of large-scale tropical extinctions, at least over the next century. Here, I summarize this controversy and describe how the debate is stimulating a serious examination of the causes and biological consequences of future tropical deforestation.},
-author = {Laurance, W F},
-file = {::},
-journal = {Trends In Ecology {\&} Evolution},
-keywords = {biodiversity,change,tropical},
-number = {2},
-pages = {65--70},
-title = {{Have we overstated the tropical biodiversity crisis?}},
-url = {tropical+diversity{\%}5CLaurance2007.PDF},
-volume = {22},
-year = {2007}
-}
-@book{leigh1999tropical,
-author = {Leigh, E G},
-isbn = {9780195096033},
-publisher = {Oxford University Press},
-title = {{Tropical Forest Ecology: A View from Barro Colorado Island}},
-url = {https://books.google.be/books?id=1knnCwAAQBAJ},
-year = {1999}
-}
-@article{hsieh2016inext,
-author = {Hsieh, T C and Ma, K H and Chao, Anne},
-journal = {Methods in Ecology and Evolution},
-number = {12},
-pages = {1451--1456},
-publisher = {Wiley Online Library},
-title = {{iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)}},
-volume = {7},
-year = {2016}
-}
-@article{Degen2006,
-abstract = {Over-exploitation and fragmentation are serious problems for tropical forests. Most sustainable forest management practices avoid clear-cuts and apply selective logging systems focused on a few commercial species. We applied a simulation model to estimate the impact of such selective logging scenarios on the genetic diversity and demography of four tropical tree species from French Guiana. The simulations used data on genetic and demographic composition, growth, phenology and pollen and seed dispersal obtained for Dicorynia guianensis, Sextonia rubra, Symphonia globulifera and Vouacapoua americana at the experimental site in Paracou. Whereas Symphonia globulifera serves as a model for a species with low logging pressure, the other three species represent the most exploited tree species in French Guiana. In simulations with moderate logging, typical for French Guiana, with large cutting diameter ({\textgreater}60 cm diameter) and long cutting cycles (65 years), the two species V. americana and Sextonia rubra were not able to recover their initial stock at the end of the rotation period, with a large decrease in the number of individuals and in basal area. Under a more intensive logging system (cutting diameter {\textgreater}45 cm diameter, cutting cycles of 30 years) that is common practice in the Brazilian Amazon, only Symphonia globulifera showed no negative impact. Generally, the differences between the genetic parameters in the control scenarios without logging and the logging scenarios were surprisingly small. The main reasons for this were the overlapping of generations and the effective dispersal ability of gene vectors in all species, which guarantee relative homogeneity of the genetic structure in different age classes. Nevertheless, decreasing the population size by logging reduced the number of genotypes and caused higher genetic distances between the original population and the population at the end of the logging cycles. Sensitivity analysis showed that genetic changes in the logging scenarios were principally determined by the growth, densities and cutting diameter of each species, and only to a very small extent by the reproductive system including factors such as pollen and seed dispersal and flowering phenology. {\textcopyright} 2006 Elsevier Ltd. All rights reserved.},
-author = {Degen, B. and Blanc, L. and Caron, H. and Maggia, L. and Kremer, A. and Gourlet-Fleury, S.},
-doi = {10.1016/j.biocon.2006.02.014},
-file = {::},
-isbn = {0006-3207},
-issn = {00063207},
-journal = {Biological Conservation},
-keywords = {Demography,Genetic diversity,Logging,Phenology,Pollen and seed dispersal,Simulation,Trees,Tropics},
-number = {3},
-pages = {386--401},
-pmid = {239139400004},
-title = {{Impact of selective logging on genetic composition and demographic structure of four tropical tree species}},
-volume = {131},
-year = {2006}
-}
-@article{Chao2014,
-abstract = {Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number qD, where q = 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q {\textgreater} 0) and present a unified approach for both individual-based (abundance) data and samplebased (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q = 0 (species richness), q = 1 (the exponential of Shannon's entropy index), and q = 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants. {\textcopyright} 2014 by the Ecological Society of America.},
-archivePrefix = {arXiv},
-arxivId = {1075},
-author = {Chao, Anne and Gotelli, Nicholas J. and Hsieh, T. C. and Sander, Elizabeth L. and Ma, K. H. and Colwell, Robert K. and Ellison, Aaron M.},
-doi = {10.1890/13-0133.1},
-eprint = {1075},
-file = {::},
-isbn = {0012-9615},
-issn = {00129615},
-journal = {Ecological Monographs},
-keywords = {Abundance data,Diversity,Extrapolation,Hill numbers,Incidence data,Interpolation,Prediction,Rarefaction,Sample coverage,Species richness},
-number = {1},
-pages = {45--67},
-pmid = {21769936},
-title = {{Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies}},
-volume = {84},
-year = {2014}
-}
-@article{Marcon2014c,
-abstract = {entropart is a package for R designed to estimate diversity based on HCDT entropy or similarity-based entropy. It allows calculating species-neutral, phylogenetic and functional entropy and diversity, partitioning them and correcting them for estimation bias.},
-author = {Marcon, Eric and H{\'{e}}rault, Bruno},
-doi = {10.18637/jss.v067.i08},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Marcon, H{\'{e}}rault - 2015 - entropart, an R Package to Measure and Partition Diversity.pdf:pdf},
-journal = {Journal of Statistical Software},
-number = {8},
-pages = {1--26},
-title = {{entropart, an R Package to Measure and Partition Diversity}},
-url = {http://cran.r-project.org/package=entropart},
-volume = {67},
-year = {2015}
-}
-@book{Gourlet-Fleury2004,
-address = {Paris},
-author = {Gourlet-Fleury, Sylvie and Guehl, Jean Marc and Laroussinie, OIivier},
-publisher = {Elsevier},
-title = {{Ecology {\&} management of a neotropical rainforest. Lessons drawn from Paracou, a long-term experimental research site in French Guiana}},
-year = {2004}
-}
-@book{Lindsay2011,
-author = {Lindsay, David},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Lindsay - 2011 - Scientific Writing =Thinking in Words.pdf:pdf},
-isbn = {0643100466,9780643100466},
-publisher = {CSIRO Publishing},
-title = {{Scientific Writing =Thinking in Words}},
-year = {2011}
-}
-@article{Tothmeresz1995,
-abstract = {The measurement of diversity, one of the most important concepts in present-day ecology, can be improved by methods of diversity ordering which have recently been developed. This ordering is achieved by aD(alpha) diversity index family. Indices of this family show varying sensitivities to the rare and abundant species as the scale parameter, alpha, changes. The aim of this paper is to review and assess 12 methods of diversity ordering and discuss their relationships in detail. Two of the methods are new to the ecological literature. The diversity ordering methods are compared as to their effectiveness in graphically displaying the differences of community structure and demonstrating the (non-)comparability of communities. Small, medium and large data sets were used to evaluate the methods. A small artificial data set (five to seven species) and a large semi-artificial data set (31 - 141 species) are used in this paper. The results suggest that Renyi's diversity index family and Logarithmic dominance ordering are the most useful methods for diversity ordering of communities of all sizes. Right-tailsum diversity ordering performs well for small communities.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {T{\'{o}}thm{\'{e}}r{\'{e}}sz, B{\'{e}}la},
-doi = {10.2307/3236223},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {1100-9233},
-issn = {11009233},
-journal = {Journal of Vegetation Science},
-keywords = {compari-,diversity family,diversity profile,diversity profiles and their,eter diversity,introduction,one-param-,r{\'{e}}nyi,s diversity index},
-number = {2},
-pages = {283--290},
-pmid = {471},
-title = {{Comparison of different methods for diversity ordering}},
-url = {http://doi.wiley.com/10.2307/3236223},
-volume = {6},
-year = {1995}
-}
-@article{Coste2010b,
-abstract = {Chlorophyll meters such as the SPAD-502 offer a simple, inexpensive and rapid method to estimate foliar chlorophyll content. However, values provided by SPAD-502 are unitless and require empirical calibrations between SPAD units and extracted chlorophyll values. Leaves of 13 tree species from the tropical rain forest in French Guiana were sampled to select the most appropriate calibration model among the often-used linear, polynomial and exponential models, in addition to a novel homographic model that has a natural asymptote. The homographic model best accurately predicted total chlorophyll content (mu g cm(-2)) from SPAD units (R-2 = 0.89). Interspecific differences in the homographic model parameters explain less than 7{\%} of the variation in chlorophyll content in our data set. The utility of the general homographic model for a variety of research and management applications clearly outweighs the slight loss of model accuracy due to the abandon of the species' effect.},
-annote = {From Duplicate 2 ( Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter: a calibration test with thirteen tree species of tropical rainforest in French Guiana - Coste, Sabrina; Baraloto, Christopher; Leroy, C{\'{e}}line; Marcon, {\'{E}}ric; Renaud, Am{\'{e}}lie; Richardson, Andrew D; Roggy, Jean-Christophe; Schimann, Heidy; Uddling, Johan; H{\'{e}}rault, Bruno )
-
-ISI Document Delivery No.: 656QA
-Times Cited: 0
-Cited Reference Count: 20
-Coste, Sabrina Baraloto, Christopher Leroy, Celine Marcon, Eric Renaud, Amelie Richardson, Andrew D. Roggy, Jean-Christophe Schimann, Heidy Uddling, Johan Herault, Bruno
-EDP SCIENCES S A
-LES ULIS CEDEX A},
-author = {Coste, Sabrina and Baraloto, Christopher and Leroy, C{\'{e}}line and Marcon, Eric and Renaud, Am{\'{e}}lie and Richardson, Andrew D. and Roggy, Jean-Christophe and Schimann, Heidy and Uddling, Johan and H{\'{e}}rault, Bruno},
-doi = {10.1051/forest/2010020},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Coste et al. - 2010 - Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter a calibration test with thirteen tree sp.pdf:pdf},
-journal = {Annals of Forest Science},
-number = {6},
-pages = {607},
-title = {{Assessing foliar chlorophyll contents with the SPAD-502 chlorophyll meter: a calibration test with thirteen tree species of tropical rainforest in French Guiana}},
-url = {http://link.springer.com/10.1051/forest/2010020},
-volume = {67},
-year = {2010}
-}
-@incollection{Charles-Dominique2001,
-abstract = {The Nouragues tropical forest research station was established in 1986 to implement research on the natural mechanisms of forest regeneration. We chose to select a place relatively removed from rivers (navigable water courses) but yet not too far from Cayenne (for obvious financial reasons) and close to a pre-existent light research camp established by the National Museum of Natural History on the Parar{\'{e}} rapids of the Arataye river. Both the fauna and flora of this area had been under study since 1978, and this provided a valuable scientific data base on which to build further research.},
-address = {Dordrecht},
-author = {Charles-Dominique, Pierre},
-booktitle = {Nouragues: Dynamics and Plant-Animal Interactions in a Neotropical Rainforest},
-doi = {10.1007/978-94-015-9821-7_1},
-editor = {Bongers, Frans and Charles-Dominique, Pierre and Forget, Pierre-Michel and Th{\'{e}}ry, Marc},
-isbn = {978-94-015-9821-7},
-pages = {1--8},
-publisher = {Springer Netherlands},
-title = {{The Field Station BT}},
-url = {https://doi.org/10.1007/978-94-015-9821-7{\_}1},
-year = {2001}
-}
-@article{Noss1999,
-abstract = {Enlightened forest management requires reliable information on the status and condition of each forest - interpreted from a broad context - and of change in forest conditions over time. The process of forest planning must begin with a clear statement of goals, from which detailed objectives and management plans follow. Goals and objectives for forest management should reflect the conservation value of a forest relative to other forests of the same general type. This paper reviews some recent assessments (with emphasis on North America), presents a framework for forest assessment and monitoring, and suggests some indicators of biodiversity in forests. Among the broad assessments of forest status and conservation value are a global 'forest frontiers' assessment by the World Resources Institute, gap analysis projects that assess the level of representation of forests and other communities in protected areas, and ecoregion-based conservation assessments conducted by the World Wildlife Fund. Also important is information on change in forest area and condition over time. Among the common changes in forests over the past two centuries are loss of old forests, simplification of forest structure, decreasing size of forest patches, increasing isolation of patches, disruption of natural fire regimes, and increased road building, all of which have had negative effects on native biodiversity. These trends can be reversed, or at least slowed, through better management. Progress toward forest recovery can be measured through the use of ecological indicators that correspond to the specific conditions and trends of concern. Although there is a wealth of indicators to choose from, most have been poorly tested and require rigorous validation in order to be interpreted with confidence.},
-author = {Noss, Reed F.},
-doi = {10.1016/S0378-1127(98)00394-6},
-file = {::},
-isbn = {1541757068},
-issn = {03781127},
-journal = {Forest Ecology and Management},
-keywords = {Assessment,Biodiversity,Forests,Indicators,Monitoring},
-number = {2-3},
-pages = {135--146},
-pmid = {22059587},
-title = {{Assessing and monitoring forest biodiversity: A suggested framework and indicators}},
-volume = {115},
-year = {1999}
-}
-@article{Condit1995,
-abstract = {The past 15 years has seen the creation oflarge ({\textgreater}/16 ha) permanent inventory plots in each of the major tropical forest formations of the world. Currently, six such plots have been fully mapped, and five more and under way. A standardized methodology is used at all sites - a complete census of all trees and saplings down to 1 cm in diameter - thus assuring strict comparability between sites and allowing the development of general models for the dynamics of tropical forests. The inventories aim to gather demographic information on individual tree species, to provide long-term information on forest composition so that future changes can be detected, to estimate the economic value of forest resources, to generate models of sustainable extraction, and to provide data on underused native species for use in reforestation or plantation forestry. The plots also provide data from undisturbed forest to serve as a control for anthropological and management studies of harvested forests. {\textcopyright} 1995.},
-author = {Condit, Richard},
-doi = {10.1016/S0169-5347(00)88955-7},
-file = {::},
-isbn = {0169-5347},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-number = {1},
-pages = {18--22},
-pmid = {21236939},
-title = {{Research in large, long-term tropical forest plots}},
-volume = {10},
-year = {1995}
-}
-@article{Bierregaard1992,
-archivePrefix = {arXiv},
-arxivId = {089},
-author = {Bierregaard, Richard O. and Lovejoy, Thoma E. and Kapos, Valerie and dos Santos, Augusto Angelo and Hutchings, Roger W.},
-doi = {10.2307/1312085},
-eprint = {089},
-file = {::},
-issn = {00063568},
-journal = {BioScience},
-number = {11},
-pages = {859--866},
-title = {{The biological dynamics of tropical rainforest fragments : a prospective comparison of fragments and continuous forest . The biological dynamics of tropical rainforest fragments : a prospective comparison of fragments and continuous forest .}},
-volume = {42},
-year = {1992}
-}
-@article{oksanen2010vegan,
-author = {Oksanen, Jari and Blanchet, F Guillaume and Kindt, Roeland and Legendre, Pierre and O�hara, R B and Simpson, Gavin L and Solymos, Peter and Stevens, M Henry H and Wagner, Helene},
-journal = {R Development Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing},
-title = {{vegan: Community Ecology Package. R package version 1.17-2}},
-year = {2010}
-}
-@book{R,
-address = {Vienna, Austria},
-author = {{R Core Team}},
-isbn = {3-900051-07-0},
-publisher = {R Foundation for Statistical Computing},
-title = {{R: A Language and Environment for Statistical Computing}},
-url = {http://www.r-project.org},
-year = {2018}
-}
-@unpublished{marcon:cel-01205813,
-address = {Kourou, France},
-annote = {Lecture},
-author = {Marcon, Eric},
-institution = {AgroParisTech},
-keywords = {diversit{\'{e}} beta ; diversit{\'{e}} gamma ; phylog{\'{e}}nie ; di},
-month = {sep},
-title = {{Mesures de la Biodiversit{\'{e}}}},
-type = {Master},
-url = {https://hal-agroparistech.archives-ouvertes.fr/cel-01205813},
-year = {2015}
-}
-@article{Molino2001,
-abstract = {The “intermediate disturbance hypothesis”, which postulates maximum diversity at intermediate regimes of disturbance, has never been clearly proved to apply to species-rich tropical forest tree communities and to local-scale canopy disturbances that modify light environments. This hypothesis was tested on a sample of 17,000 trees in a Guianan forest, 10 years after a silvicultural experiment that added to natural treefall gaps a wide range of disturbance intensities. Species richness, standardized to eliminate density effects, peaked at intermediate disturbance levels, particularly when disturbance intensity was estimated through the percentage of stems of strongly light-dependent species.},
-author = {Molino, Jean-Fran{\c{c}}ois and Sabatier, Daniel},
-doi = {10.1126/science.1060284},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Molino, Sabatier - 2001 - Tree diversity in tropical rain forests a validation of the intermediate disturbance hypothesis.pdf:pdf},
-journal = {Science},
-number = {5547},
-pages = {1702--1704},
-title = {{Tree diversity in tropical rain forests: a validation of the intermediate disturbance hypothesis}},
-url = {http://www.sciencemag.org/cgi/content/full/294/5547/1702},
-volume = {294},
-year = {2001}
-}
-@article{Condit2014,
-abstract = {The Center for Tropical Forest Science established a network of 50-ha forest inventory plots in the 1980s, and now assists local scientists with field and database methods at 44 large-scale plots across boreal, temperate, and tropical forest biomes. We published detailed field methods over a decade ago, but at that time, data were maintained in spreadsheet-like formats, most harboring design flaws that resulted in frequent errors. We since established detailed database methods and a normalized data model for housing multiple censuses of large plots. Our largest databases include {\textgreater}2 million measurements, and each has a master version on a server where all collaborators can access and edit data. This paper focuses on the data requirements for handling tree census data and how to design databases to meet these requirements and to ensure data integrity. There are six key elements of a tree census which the database must reflect: (1) measurements, including individual trees (genetic units), stems within trees, and multiple measurements of stems; both field and data methods must assure that every tree, stem, and measurement is precisely identified and can be relocated easily; (2) coordinates, including quadrats within a plot, because field mapping is usually done by assigning x- y coordinates relative to local quadrat markers; (3) taxonomy, carrying a species identity for every tree with a history of individual re-identifications; (4) personnel, with records of the people who performed field and data work per quadrat; (5) assessment of field error via random re-measurements; and (6) a log of changes and a system of archiving so that errors can be tracked and past versions can be reconstructed and cited in publications. A well-designed database model reduces a variety of integrity errors and improves access to data tables in identical formats across many plots, allowing data analyses to be easily replicated and results to be compared. The principal disadvantage is that complexity of the database requires experienced data managers. {\textcopyright} 2013.},
-author = {Condit, Richard and Lao, Suzanne and Singh, Anudeep and Esufali, Shameema and Dolins, Steven},
-doi = {10.1016/j.foreco.2013.09.011},
-file = {::},
-isbn = {03781127},
-issn = {03781127},
-journal = {Forest Ecology and Management},
-keywords = {Forest plot database,Integrity errors,Normalized data,Tree census},
-pages = {21--31},
-title = {{Data and database standards for permanent forest plots in a global network}},
-volume = {316},
-year = {2014}
-}
-@article{Frankham1997,
-abstract = {Island populations are much more prone to extinction than mainland populations. The reasons for this remain controversial. If inbreeding and loss of genetic variation are involved, then genetic variation must be lower on average in island than mainland populations. Published data on levels of genetic variation for allozymes, nuclear DNA markers, mitochondrial DNA, inversions and quantitative characters in island and mainland populations were analysed. A large and highly significant majority of island populations have less allozyme genetic variation than their mainland counterparts (165 of 202 comparisons), the average reduction being 29 per cent. The magnitude of differences was related to dispersal ability. There were related differences for all the other measures. Island endemic species showed lower genetic variation than related mainland species in 34 of 38 cases. The proportionate reduction in genetic variation was significantly greater in island endemic than in nonendemic island populations in mammals and birds, but not in insects. Genetic factors cannot be discounted as a cause of higher extinction rates of island than mainland populations.},
-archivePrefix = {arXiv},
-arxivId = {Thesid$\backslash$Genetic Diversity},
-author = {Frankham, R.},
-doi = {10.1038/sj.hdy.6880980},
-eprint = {Thesid$\backslash$Genetic Diversity},
-file = {::},
-isbn = {0018-067X},
-issn = {0018067X},
-journal = {Heredity},
-keywords = {allozymes,conservation,endemic species,extinction,genetic variation,islands},
-number = {3},
-pages = {311--327},
-pmid = {9119706},
-title = {{Do island populations have less genetic variation than mainland populations?}},
-volume = {78},
-year = {1997}
-}
-@article{BRV:BRV510,
-author = {MacArthur, Robert H},
-doi = {10.1111/j.1469-185X.1965.tb00815.x},
-issn = {1469-185X},
-journal = {Biological Reviews},
-number = {4},
-pages = {510--533},
-publisher = {Blackwell Publishing Ltd},
-title = {{Patterns of Species Diversity}},
-url = {http://dx.doi.org/10.1111/j.1469-185X.1965.tb00815.x},
-volume = {40},
-year = {1965}
-}
-@misc{STRI2018,
-author = {Institute, Smithsonian Tropical Research},
-title = {{Barro Colorado Island}},
-url = {http://www.stri.si.edu/english/research/facilities/terrestrial/barro{\_}colorado/index.php}
-}
-@article{Baraloto2010,
-abstract = {Ecology Letters (2010) 13: 1338–1347 $\backslash$nAbstract$\backslash$nCross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy towards a whole-plant approach by integrating data on functional traits for 13 448 leaves and wood tissues from 4672 trees representing 668 species of Neotropical trees. Strong correlations amongst traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover vs. costly physical leaf structure with a long revenue stream. A second axis of variation, the ‘stem economics spectrum', defines a similar tradeoff at the stem level: dense wood vs. high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.},
-author = {Baraloto, Christopher and Paine, C. E Timothy and Poorter, Lourens and Beauchene, Jacques and Bonal, Damien and Domenach, Anne Marie and H{\'{e}}rault, Bruno and Pati{\~{n}}o, Sandra and Roggy, Jean Christophe and Chave, Jerome},
-doi = {10.1111/j.1461-0248.2010.01517.x},
-file = {::},
-isbn = {1461-023X},
-issn = {14610248},
-journal = {Ecology Letters},
-keywords = {Functional diversity,Leaf economics,Multiple factor analysis,Plant strategies,Plant traits,Tropical forest,Wood density},
-number = {11},
-pages = {1338--1347},
-pmid = {20807232},
-title = {{Decoupled leaf and stem economics in rain forest trees}},
-volume = {13},
-year = {2010}
-}
-@article{Violle2011,
-abstract = {Local species coexistence is the outcome of abiotic and biotic filtering processes which sort species according to their trait values. However, the capacity of trait-based approaches to predict the variation in realized species richness remains to be investigated. In this study, we asked whether a limited number of plant functional traits, related to the leaf-height-seed strategy scheme and averaged at the community level, is able to predict the variation in species richness over a flooding disturbance gradient. We further investigated how these mean community traits are able to quantify the strength of abiotic and biotic processes involved in the disturbance-productivity-diversity relationship. We thus tested the proposal that the deviation between the fundamental species richness, assessed from ecological niche-based models, and realized species richness, i.e. field-observed richness, is controlled by species interactions. Flooding regime was determined using a detailed hydrological model. A precise vegetation sampling was performed across 222 quadrats located throughout the flooding gradient. Three core functional traits were considered: specific leaf area (SLA), plant height and seed mass. Species richness showed a hump-shaped response to disturbance and productivity, but was better predicted by only two mean community traits: SLA and height. On the one hand, community SLA that increased with flooding, controlled the disturbance-diversity relationship through habitat filtering. On the other hand, species interactions, the strength of which was captured by community height values, played a strong consistent role throughout the disturbance gradient by reducing the local species richness. Our study highlights that a limited number of simple, quantitative, easily measurable functional traits can capture the variation in plant species richness at a local scale and provides a promising quantification of key community assembly mechanisms.},
-author = {Violle, Cyrille and Bonis, Anne and Plantegenest, Manuel and Cudennec, Christophe and Damgaard, Christian and Marion, Beno{\^{i}}t and {Le C{\oe}ur}, Didier and Bouzill{\'{e}}, Jan Bernard},
-doi = {10.1111/j.1600-0706.2010.18525.x},
-file = {::},
-isbn = {1600-0706},
-issn = {00301299},
-journal = {Oikos},
-number = {3},
-pages = {389--398},
-pmid = {21672121},
-title = {{Plant functional traits capture species richness variations along a flooding gradient}},
-volume = {120},
-year = {2011}
-}
-@article{Blonder2016a,
-abstract = {Hypervolumes are used widely to conceptualize niches and trait distributions for both species and communities. Some hypervolumes are expected to be convex, with boundaries defined by only upper and lower limits (e.g., fundamental niches), while others are expected to be maximal, with boundaries defined by the limits of available space (e.g., potential niches). However, observed hypervol-umes (e.g., realized niches) could also have holes, defined as unoccu-pied hyperspace representing deviations from these expectations that may indicate unconsidered ecological or evolutionary processes. De-tecting holes in more than two dimensions has to date not been possi-ble. I develop a mathematical approach, implemented in the hyper-volume R package, to infer holes in large and high-dimensional data sets. As a demonstration analysis, I assess evidence for vacant niches in a Galapagos finch community on Isabela Island. These mathematical concepts and software tools for detecting holes provide approaches for addressing contemporary research questions across ecology and evolu-tionary biology.},
-author = {Blonder, Benjamin},
-doi = {10.1086/685444},
-file = {::},
-issn = {0003-0147},
-journal = {The American Naturalist},
-keywords = {geometry,hole,hutchinson,hypervolume,niche,vacant},
-number = {4},
-pages = {E93--E105},
-pmid = {27028084},
-title = {{Do Hypervolumes Have Holes?}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/685444},
-volume = {187},
-year = {2016}
-}
-@article{Albert2011,
-abstract = {Trait-based studies have become extremely common in plant ecology. Trait-based approaches often rely on the tacit assumption that intraspecific trait variability (ITV) is negligible compared to interspecific variability, so that species can be characterized by mean trait values. Yet, numerous recent studies have challenged this assumption by showing that ITV significantly affects various ecological processes. Accounting for ITV may thus strengthen trait-based approaches, but measuring trait values on a large number of individuals per species and site is not feasible. Therefore, it is important and timely to synthesize existing knowledge on ITV in order to (1) decide critically when ITV should be considered, and (2) establish methods for incorporating this variability. Here we propose a practical set of rules to identify circumstances under which ITV should be accounted for. We formulate a spatial trait variance partitioning hypothesis to highlight the spatial scales at which ITV cannot be ignored in ecological studies. We then refine a set of four consecutive questions on the research question, the spatial scale, the sampling design, and the type of studied traits, to determine case-by-case if a given study should quantify ITV and test its effects. We review methods for quantifying ITV and develop a step-by-step guideline to design and interpret simulation studies that test for the importance of ITV. Even in the absence of quantitative knowledge on ITV, its effects can be assessed by varying trait values within species within realistic bounds around the known mean values. We finish with a discussion of future requirements to further incorporate ITV within trait-based approaches. This paper thus delineates a general framework to account for ITV and suggests a direction towards a more quantitative trait-based ecology. {\textcopyright} 2011.},
-author = {Albert, C{\'{e}}cile H. and Grassein, Fabrice and Schurr, Frank M. and Vieilledent, Ghislain and Violle, Cyrille},
-doi = {10.1016/j.ppees.2011.04.003},
-file = {::},
-isbn = {1433-8319},
-issn = {14338319},
-journal = {Perspectives in Plant Ecology, Evolution and Systematics},
-keywords = {Comparative ecology,Functional ecology,Genetic variability,Intraspecific functional variability,Phenotypic plasticity,Plant functional traits,Within-species variability},
-number = {3},
-pages = {217--225},
-title = {{When and how should intraspecific variability be considered in trait-based plant ecology?}},
-volume = {13},
-year = {2011}
-}
-@article{Chesson2000a,
-abstract = {▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...},
-archivePrefix = {arXiv},
-arxivId = {10.1146/annurev.ecolsys.31.1.343},
-author = {Chesson, Peter},
-doi = {10.1146/annurev.ecolsys.31.1.343},
-eprint = {annurev.ecolsys.31.1.343},
-file = {::},
-isbn = {0309051908},
-issn = {0066-4162},
-journal = {Annual Review of Ecology and Systematics},
-keywords = {coexistence,competition,niche,predation,spatial and temporal variation.},
-month = {nov},
-number = {1},
-pages = {343--366},
-pmid = {10966460},
-primaryClass = {10.1146},
-publisher = {Annual Reviews 4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA},
-title = {{Mechanisms of Maintenance of Species Diversity}},
-url = {http://www.annualreviews.org/doi/10.1146/annurev.ecolsys.31.1.343},
-volume = {31},
-year = {2000}
-}
-@article{Navas2010,
-author = {Navas, M},
-doi = {10.1046/j.0028-646x.2001.00239.x},
-file = {::},
-issn = {0028646X},
-journal = {New Phytologist},
-keywords = {152,2001,69,83,functional leaf traits,leaf dry matter content,leaf nitrogen concentration,mediterranean old fields,new phytologist,plant functional classification,spatio-temporal variability,specific leaf area,structure-function relationships},
-number = {1},
-pages = {69--83},
-title = {{Consistency leaf traits species ranking based on functional leaf traits}},
-volume = {152},
-year = {2010}
-}
-@article{Albert2012,
-abstract = {Functional diversity (FD) is a key facet of biodiversity used to address$\backslash$ncentral questions in ecology. Despite recent methodological advances, FD$\backslash$nremains a complex concept and no consensus has been reached either on$\backslash$nhow to quantify it, or on how it influences ecological processes. Here$\backslash$nwe define FD as the distribution of trait values within a community.$\backslash$nWhen and how to account for intraspecific trait variability (ITV) when$\backslash$nmeasuring FD remains one of the main current debates. It remains however$\backslash$nunclear to what extent accounting for population-level ITV would modify$\backslash$nFD quantification and associated conclusions. In this paper, we address$\backslash$ntwo critical questions: (1) How sensitive are different components of FD$\backslash$nto the inclusion of population-level ITV? (2) Does the omission of ITV$\backslash$nobscure the understanding of ecological patterns? Using a mixture of$\backslash$nempirical data and simulation experiments, we conducted a sensitivity$\backslash$nanalysis of four commonly used FD indices (community weighted mean$\backslash$ntraits, functional richness, Rao's quadratic entropy, Petchey and$\backslash$nGaston's FD index) and their relationships with environmental gradients$\backslash$nand species richness, by varying both the extent (plasticity or not) and$\backslash$nthe structure (contingency to environmental gradient due to local$\backslash$nadaptation) of population-level ITV. Our results suggest that ITV may$\backslash$nstrongly alter the quantification of FD and the detection of ecological$\backslash$npatterns. Our analysis highlights that 1) species trait values$\backslash$ndistributions within communities are crucial to the sensitivity to ITV,$\backslash$n2) ITV structure plays a major role in this sensitivity and 3) different$\backslash$nindices are not evenly sensitive to ITV, the single-trait FD from$\backslash$nPetchey and Gaston being the most sensitive among the four metrics$\backslash$ntested. We conclude that the effects of intraspecific variability in$\backslash$ntrait values should be more systematically tested before drawing central$\backslash$nconclusions on FD, and suggest the use of simulation studies for such$\backslash$nsensitivity analyses.},
-author = {Albert, C{\'{e}}cile H. and de Bello, Francesco and Boulangeat, Isabelle and Pellet, Gilles and Lavorel, Sandra and Thuiller, Wilfried},
-doi = {10.1111/j.1600-0706.2011.19672.x},
-file = {::},
-isbn = {0030-1299},
-issn = {00301299},
-journal = {Oikos},
-number = {1},
-pages = {116--126},
-title = {{On the importance of intraspecific variability for the quantification of functional diversity}},
-volume = {121},
-year = {2012}
-}
-@article{DeQueiroz2007a,
-abstract = {The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.},
-archivePrefix = {arXiv},
-arxivId = {NIHMS150003},
-author = {{De Queiroz}, Kevin},
-doi = {10.1080/10635150701701083},
-eprint = {NIHMS150003},
-file = {::},
-isbn = {1063-5157},
-issn = {10635157},
-journal = {Systematic Biology},
-keywords = {Species concept,Species criteria,Species delimitation},
-number = {6},
-pages = {879--886},
-pmid = {18027281},
-title = {{Species concepts and species delimitation}},
-volume = {56},
-year = {2007}
-}
-@article{Siefert2015b,
-abstract = {Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25{\%} of the total trait variation within communities and 32{\%} of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.},
-author = {Siefert, Andrew and Violle, Cyrille and Chalmandrier, Lo{\"{i}}c and Albert, C{\'{e}}cile H. and Taudiere, Adrien and Fajardo, Alex and Aarssen, Lonnie W. and Baraloto, Christopher and Carlucci, Marcos B. and Cianciaruso, Marcus V. and {de L. Dantas}, Vin{\'{i}}cius and de Bello, Francesco and Duarte, Leandro D.S. and Fonseca, Carlos R. and Freschet, Gr{\'{e}}goire T. and Gaucherand, St{\'{e}}phanie and Gross, Nicolas and Hikosaka, Kouki and Jackson, Benjamin and Jung, Vincent and Kamiyama, Chiho and Katabuchi, Masatoshi and Kembel, Steven W. and Kichenin, Emilie and Kraft, Nathan J.B. and Lagerstr{\"{o}}m, Anna and Bagousse-Pinguet, Yoann Le and Li, Yuanzhi and Mason, Norman and Messier, Julie and Nakashizuka, Tohru and Overton, Jacob Mcc and Peltzer, Duane A. and P{\'{e}}rez-Ramos, I. M. and Pillar, Val{\'{e}}rio D. and Prentice, Honor C. and Richardson, Sarah and Sasaki, Takehiro and Schamp, Brandon S. and Sch{\"{o}}b, Christian and Shipley, Bill and Sundqvist, Maja and Sykes, Martin T. and Vandewalle, Marie and Wardle, David A.},
-doi = {10.1111/ele.12508},
-file = {::},
-isbn = {1461-0248},
-issn = {14610248},
-journal = {Ecology Letters},
-keywords = {Community ecology,Functional diversity,Interspecific variation,Intraspecific variability,Leaf trait,Plant functional trait,Trait-based ecology},
-number = {12},
-pages = {1406--1419},
-pmid = {26415616},
-title = {{A global meta-analysis of the relative extent of intraspecific trait variation in plant communities}},
-volume = {18},
-year = {2015}
-}
-@misc{Niklas1995,
-abstract = {The allometry of tree height with respect to trunk diameter and the allometry of trunk diameter with respect to distance from the top of the tree (i.e. trunk taper) were determined for 27 Robinia pseudoacacia trees differing in age and size growing in an open field. The allometric (scaling) exponent for height was {\textgreater} 1 for small and young trees and decreased to 2/3 and then 1/2 as tree size and age increased. Similarly, the exponent for taper was {\textgreater} 1 near the tips of young and old trunks and converged onto values of 2/3 and 1/2 toward the base of mature tree trunks. These observations indicate that a single 'optimal mechanical design principle' (i.e. elastic, stress or geometric self-similarity) neither holds true throughout the lifetime of R. pseudoacacia trees, nor does a single design principle govern the taper of a trunk throughout its entire length. Rather, over the course of growth and development, the allometry of R. pseudoacacia tree height and trunk taper progressively changes, complying with geometric self-similarity for young plants (and young portions of old plants) and subsequently giving the appearance of elastic or stress self-similarity as plants (or portions of plants) get older and therefore larger. Analyses of published (and new) data suggest that the conclusions drawn for R. pseudoacacia trees are likely to hold true for other tree species because stem growth in diameter is 'indeterminate' whereas growth in overall tree height is asymptotic and therefore essentially 'determinate'. {\textcopyright} 1995 Annals of Botany Company.},
-author = {Niklas, Karl J.},
-booktitle = {Annals of Botany},
-doi = {10.1006/anbo.1995.1015},
-file = {::},
-isbn = {0305-7364},
-issn = {10958290},
-keywords = {Robinia pseudoacacia,Scaling,Woody plants},
-number = {3},
-pages = {217--227},
-pmid = {1290},
-title = {{Size-dependent allometry of tree height, diameter and trunk-taper}},
-volume = {75},
-year = {1995}
-}
-@article{Escudero2016,
-abstract = {Functional traits are the center of recent attempts to unify key ecological theories on species coexistence and assembling in populations and communities. While the plethora of studies on the role of functional traits to explain patterns and dynamics of communities has rendered a complex picture due to the idiosyncrasies of each study system and approach, there is increasing evidence on their actual relevance when aspects such as different spatial scales, intraspecific variability and demography are considered.},
-author = {Escudero, Adri{\'{a}}n and Valladares, Fernando},
-doi = {10.1007/s00442-016-3578-5},
-file = {::},
-isbn = {1432-1939},
-issn = {00298549},
-journal = {Oecologia},
-number = {4},
-pages = {919--922},
-pmid = {26897604},
-publisher = {Springer Berlin Heidelberg},
-title = {{Trait-based plant ecology: moving towards a unifying species coexistence theory: Features of the Special Section}},
-volume = {180},
-year = {2016}
-}
-@article{Hacke2015,
-abstract = {Cohesion-tension transport of water is an energetically efficient way to carry large amounts of water from the roots up to the leaves. However, the cohesion-tension mechanism places the xylem water under negative hydrostatic pressure (Px), rendering it susceptible to cavitation. There are conflicts among the structural requirements for minimizing cavitation on the one hand vs maximizing efficiency of transport and construction on the other. Cavitation by freeze-thaw events is triggered by in situ air bubble formation and is much more likely to occur as conduit diameter increases, creating a direct conflict between conducting efficiency and sensitivity to freezing induced xylem failure. Temperate ring-porous trees and vines with wide diameter conduits tend to have a shorter growing season than conifers and diffuse-porous trees with narrow conduits. Cavitation by water stress occurs by air seeding at interconduit pit membranes. Pit membrane structure is at least partially uncoupled from conduit size, leading to a much less pronounced trade-off between conducting efficiency and cavitation by drought than by freezing. Although wider conduits are generally more susceptible to drought-induced cavitation within an organ, across organs or species this trend is very weak. Different trade-offs become apparent at the level of the pit membranes that interconnect neighbouring conduits. Increasing porosity of pit membranes should enhance conductance but also make conduits more susceptible to air seeding. Increasing the size or number of pit membranes would also enhance conductance, but may weaken the strength of the conduit wall against implosion. The need to avoid conduit collapse under negative pressure creates a significant trade-off between cavitation resistance and xylem construction cost, as revealed by relationships between conduit wall strength, wood density and cavitation pressure. Trade-offs involving cavitation resistance may explain the correlations between wood anatomy, cavitation resistance, and the physiological range of negative pressure experienced by species in their native habitats.},
-author = {Hacke, Uwe},
-doi = {10.1007/978-3-319-15783-2},
-file = {::},
-isbn = {9783319157832},
-issn = {14338319},
-journal = {Functional and Ecological Xylem Anatomy},
-keywords = {cavitation,drought stress,ecological wood anatomy,freezing stress,stomatal control,wood density,xylem structure},
-pages = {1--281},
-title = {{Functional and ecological Xylem anatomy}},
-volume = {4},
-year = {2015}
-}
-@article{Chesson2000,
-abstract = {The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence, in which species diversity slowly decays over time, have focused almost exclusively on equalizing mechanisms. These models would be more robust if they also included stabilizing mechanisms, which arise in many and varied ways but need not be adequate for full stability of a system. Models of unstable coexistence invite a broader view of diversity maintenance incorporating species turnover.},
-author = {Chesson, Peter},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Chesson - 2000 - Mechanisms of maintenance of species diversity.pdf:pdf},
-journal = {Annual review of Ecology and Systematics},
-pages = {343--366},
-title = {{Mechanisms of maintenance of species diversity}},
-url = {http://www.jstor.org/stable/221736},
-volume = {31},
-year = {2000}
-}
-@article{Perez-Harguindeguy2013,
-abstract = {In this paper, we have reviewed how the hydraulic design of trees influences the movement of water from roots to leaves. The hydraulic architecture of trees can limit their water relations, gas exchange throughout the crown of trees, the distribution of trees over different habitats and, perhaps, even the maximum height that a particular species can achieve. Parameters of particular importance include: (1) the vulnerability of stems to drought-induced cavitation events because cavitation reduces the hydraulic conductance of stems, (2) the leaf specific conductivity of stems because it determines the pressure gradients and most negative water potentials needed to sustain evaporation from leaves, (3) the water storage capacity of tissues because this might determine the ability of trees to survive long drought periods. All of these parameters are determined by the structure and function of anatomical components of trees. Some of the ecological and physiological trade-offs of specific structures are discussed.},
-author = {P{\'{e}}rez-Harguindeguy, N. and Diaz, S. and Garnier, E. and Lavorel, S. and Poorter, H. and Jaureguiberry, P. and Bret-Harte, M.S. S. and Cornwell, W.K. K. and Craine, J.M. M. and Gurvich, D.E. E. and Urcelay, C. and Veneklaas, E.J. J. and Reich, P.B. B. and Poorter, L. and Wright, I.J. J. and Etc. and Ray, P. and Etc. and D{\'{i}}az, S. and Lavorel, S. and Poorter, H. and Jaureguiberry, P. and Bret-Harte, M.S. S. and Cornwell, W.K. K. and Craine, J.M. M. and Gurvich, D.E. E. and Urcelay, C. and Veneklaas, E.J. J. and Reich, P.B. B. and Poorter, L. and Wright, I.J. J. and Ray, P. and Enrico, L. and Pausas, J. G. and de Vos, A. C. and Buchmann, N. and Funes, G. and Qu{\'{e}}tier, F. and Hodgson, J. G. and Thompson, K. and Morgan, H. D. and ter Steege, H. and van der Heijden, M. G. A. and Sack, L. and Blonder, B. and Poschlod, P. and Vaieretti, M. V. and Conti, G. and Staver, A. C. and Aquino, S. and Cornelissen, J. H. C.},
-doi = {http://dx.doi.org/10.1071/BT12225},
-file = {::},
-isbn = {12864560 (ISSN)},
-issn = {0829-318X},
-journal = {Australian Journal of Botany},
-keywords = {allocation,allometry,assimilate,assimilats,conductivity,conduit,conduit tapering,conifers,douglas-fir,drought tolerance,frequency,hydraulic conduc-,leaf-to-sapwood ratio,model,mod{\`{e}}le,partitioning,phloem sieve cells,picea abies,ponderosa pine,puits,sapwood water,sink,source,tivity,xylem trac-,—},
-number = {34},
-pages = {167--234},
-pmid = {12511303},
-title = {{New Handbook for standardized measurment of plant functional traits worldwide}},
-url = {http://www.uv.es/jgpausas/papers/PerezHarguindeguy-2013-AJB{\_}traits-handbook2.pdf},
-volume = {61},
-year = {2013}
-}
-@article{Violle2012,
-abstract = {Despite being recognized as a promoter of diversity and a condition for local coexistence decades ago, the importance of intraspecific variance has been neglected over time in community ecology. Recently, there has been a new emphasis on intraspecific variability. Indeed, recent developments in trait-based community ecology have underlined the need to integrate variation at both the intraspecific as well as interspecific level. We introduce new T-statistics ('T' for trait), based on the comparison of intraspecific and interspecific variances of functional traits across organizational levels, to operationally incorporate intraspecific variability into community ecology theory. We show that a focus on the distribution of traits at local and regional scales combined with original analytical tools can provide unique insights into the primary forces structuring communities. {\textcopyright} 2011 Elsevier Ltd.},
-author = {Violle, Cyrille and Enquist, Brian J. and McGill, Brian J. and Jiang, Lin and Albert, C{\'{e}}cile H. and Hulshof, Catherine and Jung, Vincent and Messier, Julie},
-doi = {10.1016/j.tree.2011.11.014},
-file = {::},
-isbn = {0169-5347 (Print) 0169-5347 (Linking)},
-issn = {01695347},
-journal = {Trends in Ecology and Evolution},
-keywords = {Community assembly,Functional trait,Intraspecific variation,Mean field approach,Species coexistence,Species diversity,T-statistics,Variance},
-number = {4},
-pages = {244--252},
-pmid = {22244797},
-title = {{The return of the variance: Intraspecific variability in community ecology}},
-volume = {27},
-year = {2012}
-}
-@article{Clark2010c,
-author = {Clark, J and Bell, D and Chu, C J and Courbaud, B and Dietze, M and Hersh, M and HilleRisLambers, J and Ib{\'{a}}{\~{n}}ez, I and LaDeau, S and McMahon, S},
-file = {::},
-journal = {Ecological Monographs},
-keywords = {bayesian analysis,biodiversity,coexistence,competition,forest dynamics,hierarchical},
-number = {4},
-pages = {569--608},
-title = {{High dimensional coexistence based on individual variation: a synthesis of evidence}},
-volume = {80},
-year = {2010}
-}
-@article{Herault2011,
-abstract = {1. Functional traits are posited to explain interspecific differences in performance, but these relationships are difficult to describe for long-lived organisms such as trees, which exhibit strong ontogenetic changes in demographic rates. Here, we use a size-dependent model of tree growth to test the extent to which of 17 functional traits related to leaf and stem economics, adult stature and seed size predict the ontogenetic trajectory of tree growth.},
-author = {H{\'{e}}rault, Bruno and Bachelot, B{\'{e}}n{\'{e}}dicte and Poorter, Lourens and Rossi, Vivien and Bongers, Frans and Chave, J{\'{e}}r{\^{o}}me and Paine, C. E Timothy and Wagner, Fabien and Baraloto, Christopher},
-doi = {10.1111/j.1365-2745.2011.01883.x},
-file = {::},
-isbn = {1365-2745},
-issn = {00220477},
-journal = {Journal of Ecology},
-keywords = {Bayesian modelling,Functional traits,Growth modelling,Leaf economics,Leaf-height-seed strategy,Plant development and life-history traits,Plant strategy,Stem economics,Tropical rain forest},
-number = {6},
-pages = {1431--1440},
-pmid = {18552625},
-title = {{Functional traits shape ontogenetic growth trajectories of rain forest tree species}},
-volume = {99},
-year = {2011}
-}
-@article{freschet_evidence_2010,
-abstract = {1. A fundamental trade-off among vascular plants between traits inferring rapid resource acquisition and those leading to conservation of resources has now been accepted broadly, but is based on empirical data with a strong bias towards leaf traits. Here, we test whether interspecific variation in traits of different plant organs obeys this same trade-off and whether within-plant trade-offs are consistent between organs. 2. Thereto, we measured suites of the same chemical and structural traits from the main vegetative organs for a species set representing aquatic, riparian and terrestrial environments including the main vascular higher taxa and growth forms of a subarctic flora. The traits were chosen to have consistent relevance for plant defence and growth across organs and environments: carbon, nitrogen, phosphorus, lignin, dry matter content, pH. 3. Our analysis shows several new trait correlations across leaves, stems and roots and a striking pattern of whole-plant integrative resource economy, leading to tight correspondence between the local leaf economics spectrum and the root (r = 0.64), stem (r = 0.78) and whole-plant (r = 0.93) economics spectra. 4. Synthesis. Our findings strongly suggest that plant resource economics is consistent across species' organs in a subarctic flora. We provide thus the first evidence for a ‘plant economics spectrum' closely related to the local subarctic ‘leaf economics spectrum'. Extending that concept to other biomes is, however, necessary before any generalization might be made. In a world facing rapid vegetation change, these results nevertheless bear considerable prospects of predicting below-ground plant functions from the above-ground components alone.},
-author = {Freschet, Gr{\'{e}}goire T and Cornelissen, Johannes H C and {Van Logtestijn}, Richard S P and Aerts, Rien},
-doi = {10.1111/j.1365-2745.2009.01615.x},
-file = {::;::},
-issn = {1365-2745},
-journal = {Journal of Ecology},
-keywords = {dry matter content,growth form,nutrient content,phylogeny,plant trait,specific leaf area,terrestrial and aquatic environments,trade-off,vegetative organs},
-number = {2},
-pages = {362--373},
-title = {{Evidence of the ‘plant economics spectrum' in a subarctic flora}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2009.01615.x/abstract},
-volume = {98},
-year = {2010}
-}
-@article{Connell1978a,
-abstract = {The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.},
-archivePrefix = {arXiv},
-arxivId = {http://links.jstor.org/sici?sici=0036-8075{\%}2819780324{\%}293{\%}3A199{\%}3A4335{\%}3C1302{\%}3ADITRFA{\%}3E2.0.CO{\%}3B2-2},
-author = {Connell, J. H.},
-doi = {10.1126/science.199.4335.1302},
-eprint = {/links.jstor.org/sici?sici=0036-8075{\%}2819780324{\%}293{\%}3A199{\%}3A4335{\%}3C1302{\%}3ADITRFA{\%}3E2.0.CO{\%}3B2-2},
-isbn = {0036-8075 (Print)$\backslash$r0036-8075 (Linking)},
-issn = {0036-8075},
-journal = {Science},
-number = {4335},
-pages = {1302--1310},
-pmid = {17840770},
-primaryClass = {http:},
-title = {{Diversity in Tropical Rain Forests and Coral Reefs}},
-url = {http://www.sciencemag.org/cgi/doi/10.1126/science.199.4335.1302},
-volume = {199},
-year = {1978}
-}
-@article{Abakumova2016,
-abstract = {Plant functional traits can vary widely as a result of phenotypic plasticity to abiotic conditions. Trait variation may also reflect responses to the identity of neighbours, although not all species are equally responsive to their biotic surroundings. We hypothesized that responses to neighbours are shaped by spatial community patterns and resulting variability in neighbour composition. More precisely, we tested the theoretical prediction that plasticity is most likely to evolve if alternative environments (in this case, different neighbour species) are common and encountered at similar frequencies. We estimated the frequencies of encountering different neighbour species in the field for 27 grassland species and measured the aboveground morphological responses of each species to conspecific vs heterospecific neighbours in a common garden. Responses to neighbour identity were dependent on how frequently the experimental neighbours were encountered by the focal species in their home community, with the greatest plasticity observed in species that encountered both neighbours (conspecific and heterospecific) with high and even frequency. Biotic interactions with neighbouring species can impose selection on plasticity in functional traits, which may feed back through trait divergence and niche differentiation to influence species coexistence and community structure.},
-author = {Abakumova, Maria and Zobel, Kristjan and Lepik, Anu and Semchenko, Marina},
-doi = {10.1111/nph.13935},
-file = {::},
-isbn = {1469-8137},
-issn = {14698137},
-journal = {New Phytologist},
-keywords = {biotic environment,competition,functional traits,local adaptation,neighbour recognition,phenotypic plasticity,selection,spatial patterns},
-month = {jul},
-number = {2},
-pages = {455--463},
-pmid = {26996338},
-title = {{Plasticity in plant functional traits is shaped by variability in neighbourhood species composition}},
-url = {http://doi.wiley.com/10.1111/nph.13935},
-volume = {211},
-year = {2016}
-}
-@article{Rozendaal2006,
-abstract = {1. The sun-shade acclimation and plasticity of 16 functional leaf traits of 38 tropical tree species were studied in relation to their light demand, maximum adult stature and ontogenetic changes in crown exposure. 2. Species differed significantly in all leaf traits, which explained a large part of the observed variation (average R-2 = 0.72). Light had a significant effect on 12 traits and species showed a similar proportional response to light, indicating that the species ranking in trait performance is largely maintained in different light environments. 3. Specific leaf area, leaf nutrient content and chlorophyll : nitrogen ratio showed the largest plasticity to irradiance. These traits are important for maximizing growth in different light conditions because they are closely linked to the photosynthetic capacity and carbon balance of the plant. 4. Plasticity is generally thought to be greatest for pioneer species that occupy early successional habitats with a large variation in irradiance. This hypothesis was rejected because short-lived pioneers showed the lowest plasticity to irradiance. 5. An alternative hypothesis states that plasticity is largest for tall species that experience large ontogenetic changes in irradiance during their life cycle. Yet plasticity was barely related to adult stature or ontogenetic changes in crown exposure. Short-lived pioneers that experience consistently high light levels did have low plasticity, but shade-tolerant species that experience consistently low light levels had high plasticity. 6. Tropical rainforest species show a large variation in plasticity. Plasticity is a compromise between many factors and constraints, and all of these may explain the observed patterns to some extent.},
-author = {Rozendaal, D. M.A. and Hurtado, V. H. and Poorter, L.},
-doi = {10.1111/j.1365-2435.2006.01105.x},
-file = {::},
-isbn = {1365-2435},
-issn = {02698463},
-journal = {Functional Ecology},
-keywords = {Acclimation,Adult stature,Bolivia,Functional leaf traits,Shade tolerance},
-number = {2},
-pages = {207--216},
-title = {{Plasticity in leaf traits of 38 tropical tree species in response to light; relationships with light demand and adult stature}},
-volume = {20},
-year = {2006}
-}
-@article{Reich2003,
-abstract = {JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. Variation in plant functional traits results from evolutionary and environmental drivers that operate at a variety of different scales, which makes it a challenge to differentiate among them. In this article we describe patterns of functional trait variation and trait correlations within and among habitats in relation to several environmental and trade-off axes. We then ask whether such patterns reflect natural selection and can be considered plant strategies. In so doing we highlight evidence that demonstrates that (1) patterns of trait variation across resource and environmental gradients (light, water, nutrients, and temperature) probably reflect adaptation, (2) plant trait variation typically involves multiple-correlated traits that arise because of inevitable trade-offs among traits and across levels of whole-plant integration and that must be understood from a whole-plant perspective, and (3) such adaptation may be globally generalizable for like conditions; i.e., the set of traits (collections of traits in syndromes) of taxa can be considered as " plant strategies. "},
-author = {Reich, P. B. and Wright, I. J. and Cavender‐Bares, J. and Craine, J. M. and Oleksyn, J. and Westoby, M. and Walters, M. B.},
-doi = {10.1086/374368},
-file = {::},
-isbn = {10585893},
-issn = {1058-5893},
-journal = {International Journal of Plant Sciences},
-keywords = {adaptation,fitness,functional groups,plant traits,selection},
-number = {S3},
-pages = {S143--S164},
-pmid = {184018500011},
-title = {{The Evolution of Plant Functional Variation: Traits, Spectra, and Strategies}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/374368},
-volume = {164},
-year = {2003}
-}
-@article{diaz_global_2015,
-abstract = {Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three- quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.},
-author = {D{\'{i}}az, Sandra and Kattge, Jens and Cornelissen, Johannes H.C. and Wright, Ian J. and Lavorel, Sandra and Dray, St{\'{e}}phane and Reu, Bj{\"{o}}rn and Kleyer, Michael and Wirth, Christian and {Colin Prentice}, I. and Garnier, Eric and B{\"{o}}nisch, Gerhard and Westoby, Mark and Poorter, Hendrik and Reich, Peter B. and Moles, Angela T. and Dickie, John and Gillison, Andrew N. and Zanne, Amy E. and Chave, J{\'{e}}r{\^{o}}me and {Joseph Wright}, S. and {Sheremet Ev}, Serge N. and Jactel, Herv{\'{e}} and Baraloto, Christopher and Cerabolini, Bruno and Pierce, Simon and Shipley, Bill and Kirkup, Donald and Casanoves, Fernando and Joswig, Julia S. and G{\"{u}}nther, Angela and Falczuk, Valeria and R{\"{u}}ger, Nadja and Mahecha, Miguel D. and Gorn{\'{e}}, Lucas D.},
-doi = {10.1038/nature16489},
-file = {::},
-isbn = {1476-4687},
-issn = {14764687},
-journal = {Nature},
-number = {7585},
-pages = {167--171},
-pmid = {26700811},
-title = {{The global spectrum of plant form and function}},
-url = {http://www.nature.com/doifinder/10.1038/nature16489},
-volume = {529},
-year = {2016}
-}
-@article{wright_worldwide_2004,
-author = {Wright, Ian J and Reich, Peter B and Westoby, Mark and Ackerly, David D and Baruch, Zdravko and Bongers, Frans and Cavender-Bares, Jeannine and Chapin, Terry and Cornelissen, Johannes H C and Diemer, Matthias and Others},
-file = {::},
-journal = {Nature},
-number = {6985},
-pages = {821--827},
-title = {{The worldwide leaf economics spectrum}},
-url = {http://www.nature.com/nature/journal/v428/n6985/abs/nature02403.html},
-volume = {428},
-year = {2004}
-}
-@article{Valladares2007,
-abstract = {Phenotypic plasticity is considered the major means by which plants cope with environmental heterogeneity. Although ubiquitous in nature, actual phenotypic plasticity is far from being maximal. This has been explained by the existence of internal limits to its expression. However, phenotypic plasticity takes place within an ecological context and plants are generally exposed to multifactor environments and to simultaneous interactions with many species. These external, ecological factors may limit phenotypic plasticity or curtail its adaptive value, but seldom have they been considered because limits to plasticity have typically addressed factors internal to the plant. We show that plastic responses to abiotic factors are reduced under situations of conservative resource use in stressful and unpredictable habitats, and that extreme levels in a given abiotic factor can negatively influence plastic responses to another factor. We illustrate how herbivory may limit plant phenotypic plasticity because damaged plants can only rarely attain the optimal phenotype in the challenging environment. Finally, it is examined how phenotypic changes involved in trait-mediated interactions can entail costs for the plant in further interactions with other species in the community. Ecological limits to plasticity must be included in any realistic approach to understand the evolution of plasticity in complex environments and to predict plant responses to global change.},
-author = {Valladares, Fernando and Gianoli, Ernesto and G{\'{o}}mez, Jos{\'{e}} M.},
-doi = {10.1111/j.1469-8137.2007.02275.x},
-file = {::},
-isbn = {0028-646X$\backslash$n1469-8137},
-issn = {0028646X},
-journal = {New Phytologist},
-keywords = {Abiotic stresses,Competition,Complex environments,Fitness,Global change,Herbivory,Phenotypic integration,Trait-mediated interactions},
-number = {4},
-pages = {749--763},
-pmid = {17997761},
-title = {{Ecological limits to plant phenotypic plasticity}},
-volume = {176},
-year = {2007}
-}
-@article{Bolnick2003,
-abstract = {Most empirical and theoretical studies of resource use and population dynamics treat conspecific individuals as ecologically equivalent. This simplification is only justified if interindividual niche variation is rare, weak, or has a trivial effect on ecological processes. This article reviews the incidence, degree, causes, and implications of individual-level niche variation to challenge these simplifications. Evidence for individual specialization is available for 93 species distributed across a broad range of taxonomic groups. Although few studies have quantified the degree to which individuals are specialized relative to their population, between-individual variation can sometimes comprise the majority of the population's niche width. The degree of individual specialization varies widely among species and among populations, reflecting a diverse array of physiological, behavioral, and ecological mechanisms that can generate intrapopulation variation. Finally, individual specialization has potentially important ecological, evolutionary, and conservation implications. Theory suggests that niche variation facilitates frequency-dependent interactions that can profoundly affect the population's stability, the amount of intraspecific competition, fitness-function shapes, and the population's capacity to diversify and speciate rapidly. Our collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Bolnick, Daniel I and Svanb{\"{a}}ck, Richard and Fordyce, James a and Yang, Louie H and Davis, Jeremy M and Hulsey, C Darrin and Forister, Matthew L},
-doi = {10.1086/343878},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {00030147},
-issn = {0003-0147},
-journal = {American Naturalist},
-keywords = {Animals,Conservation of Natural Resources,Ecology,Evolution,Genetic Variation,Models, Biological,Sample Size,Species Specificity},
-number = {1},
-pages = {1--28},
-pmid = {12650459},
-title = {{The ecology of individuals: incidence and implications of individual specialization.}},
-url = {http://www.ncbi.nlm.nih.gov/pubmed/12650459},
-volume = {161},
-year = {2003}
-}
-@article{Valladares2000,
-abstract = {The comparative phenotypic plasticity of 16 species of tropical rainforest shrubs (genus Psychotria, Rubiaceae) was investigated by growing plants in three light environments on Barro Colorado Island (BCI, Panama). The three light environments gave daily photon flux ... $\backslash$n},
-author = {Valladares, Fernando and Wright, S. Joseph and Lasso, Eloisa and Kitajima, Kaoru and Pearcy, Robert W.},
-doi = {10.1890/0012-9658(2000)081[1925:PPRTLO]2.0.CO;2},
-file = {::},
-isbn = {0012-9658},
-issn = {00129658},
-journal = {Ecology},
-keywords = {Barro Colorado Island, Panama,Leaf longevity,Light acclimation,Phenotypic plasticity,Predictability of environmental change,Psychotria,Stress syndrome,Tropical forest},
-number = {7},
-pages = {1925--1936},
-pmid = {88214400014},
-title = {{Plastic phenotypic response to light of 16 congeneric shrubs from a panamanian rainforest}},
-volume = {81},
-year = {2000}
-}
-@article{Laughlin2012,
-abstract = {Community assembly involves two antagonistic processes that select functional traits in opposite directions. Environmental filtering tends to increase the functional similarity of species within communities leading to trait convergence, whereas competition tends to limit the functional similarity of species within communities leading to trait divergence. Here, we introduce a new hierarchical Bayesian model that incorporates intraspecific trait variation into a predictive framework to unify classic coexistence theory and evolutionary biology with recent trait-based approaches. Model predictions exhibited a significant positive correlation (r = 0.66) with observed relative abundances along a 10 °C gradient in mean annual temperature. The model predicted the correct dominant species in half of the plots, and accurately reproduced species' temperature optimums. The framework is generalizable to any ecosystem as it can accommodate any species pool, any set of functional traits and multiple environmental gradients, and it eliminates some of the criticisms associated with recent trait-based community assembly models.},
-author = {Laughlin, Daniel C. and Joshi, Chaitanya and van Bodegom, Peter M. and Bastow, Zachary A. and Ful{\'{e}}, Peter Z.},
-doi = {10.1111/j.1461-0248.2012.01852.x},
-editor = {Fukami, Tadashi},
-file = {::;::},
-isbn = {1461-0248},
-issn = {1461023X},
-journal = {Ecology Letters},
-keywords = {Assembly rules,Bark thickness,Environmental filtering,Hierarchical Bayesian model,Limiting similarity,Maximum entropy,Specific leaf area,Trait convergence,Trait divergence,Wood density},
-month = {nov},
-number = {11},
-pages = {1291--1299},
-pmid = {22906233},
-title = {{A predictive model of community assembly that incorporates intraspecific trait variation}},
-url = {http://doi.wiley.com/10.1111/j.1461-0248.2012.01852.x},
-volume = {15},
-year = {2012}
-}
-@article{Messier2010a,
-abstract = {Despite the increasing importance of functional traits for the study of plant ecology, we do not know how variation in a given trait changes across ecological scales, which prevents us from assessing potential scale-dependent aspects of trait variation. To address this deficiency, we partitioned the variance in two key functional traits (leaf mass area and leaf dry matter content) across six nested ecological scales (site, plot, species, tree, strata and leaf) in lowland tropical rainforests. In both traits, the plot level shows virtually no variance despite high species turnover among plots and the size of within-species variation (leaf + strata + tree) is comparable with that of species level variation. The lack of variance at the plot level brings substantial support to the idea that trait-based environmental filtering plays a central role in plant community assembly. These results and the finding that the amount of within-species variation is comparable with interspecific variation support a shift of focus from species-based to trait-based ecology.},
-author = {Messier, Julie and McGill, Brian J. and Lechowicz, Martin J.},
-doi = {10.1111/j.1461-0248.2010.01476.x},
-file = {::},
-isbn = {1461-0248},
-issn = {1461023X},
-journal = {Ecology Letters},
-keywords = {Ecological scaling,Environmental filtering,Leaf dry matter content,Leaf functional traits,Leaf mass area,Plant community assembly,Trait-based ecology,Tropical rainforests,Variance components},
-number = {7},
-pages = {838--848},
-pmid = {20482582},
-title = {{How do traits vary across ecological scales? A case for trait-based ecology}},
-volume = {13},
-year = {2010}
-}
-@article{reich_world-wide_2014,
-abstract = {*
-The leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade-off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources.
-
-
-
-*
-Evidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages).
-
-
-
-*
-There are linkages across organs and coupling among resources, resulting in an integrated whole-plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species.
-
-
-
-*
-Economic traits influence performance and fitness consistent with trait-based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates.
-
-
-
-*
-Synthesis. Traits matter. A single ‘fast–slow' plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.},
-author = {Reich, Peter B},
-doi = {10.1111/1365-2745.12211},
-file = {::;::},
-issn = {1365-2745},
-journal = {Journal of Ecology},
-keywords = {carbon,ecophysiology,leaf,light,nutrient,phylogeny,root,stem,strategy,water},
-number = {2},
-pages = {275--301},
-shorttitle = {The world-wide ‘fast–slow' plant economics spectru},
-title = {{The world-wide ‘fast–slow' plant economics spectrum: a traits manifesto}},
-url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12211/abstract},
-volume = {102},
-year = {2014}
-}
-@article{Silvertown2004a,
-abstract = {How large numbers of competing plant species manage to coexist is a major unresolved question in community ecology. The classical explanation, that each species occupies its own niche, seems at first unlikely because most plants require the same set of resources and acquire these in a limited number of ways. However, recent studies, although few in number and incomplete in many ways, do suggest that plants segregate along various environmental niche axes, including gradients of light, soil moisture and root depth, and that partitioning of soil nutrients occurs, possibly through the mediation of microbial symbionts, some of which are more species specific than was previously thought. Although it is unlikely that niche separation along environmental axes is the only mechanism of coexistence in any large community, the evidence now suggests that it plays a more significant role than has been previously appreciated. More research into the consequences of various known tradeoffs is likely to uncover further cases of niche separation facilitating coexistence.},
-archivePrefix = {arXiv},
-arxivId = {2653},
-author = {Silvertown, Jonathan},
-doi = {10.1016/j.tree.2004.09.003},
-eprint = {2653},
-file = {::},
-isbn = {0169-5347},
-issn = {01695347},
-journal = {Trends in Ecology and Evolution},
-number = {11},
-pages = {605--611},
-pmid = {8310},
-title = {{Plant coexistence and the niche}},
-volume = {19},
-year = {2004}
-}
-@article{Niinemets2015,
-abstract = {The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept, the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10–300{\%},blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered. Although the Q. ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q. ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the withinspecies economics spectrum needs to be considered in regional- to biome-level analyses.},
-author = {Niinemets, {\"{U}}lo},
-doi = {10.1111/nph.13001},
-file = {::},
-isbn = {1469-8137},
-issn = {14698137},
-journal = {New Phytologist},
-keywords = {Bioclimatic niche,Climatic drivers,Dry mass per unit area,Leaf economics spectrum,Leaf physiognomy,Nitrogen,Photosynthesis,Trait relationships},
-number = {1},
-pages = {79--96},
-title = {{Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex}},
-volume = {205},
-year = {2015}
-}
-@article{Cornwell2006,
-abstract = {Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering.},
-author = {Cornwell, William K. and Schwilk, Dylan W. and Ackerly, David D.},
-doi = {10.1890/0012-9658(2006)87},
-file = {::},
-isbn = {0012-9658},
-issn = {00129658},
-journal = {Ecology},
-keywords = {Chaparral,Community assembly,Convex hull,Habitat filtering,Plant,Seed mass,Specific leaf area,Trait,Wood density},
-number = {6},
-pages = {1465--1471},
-pmid = {16761609},
-title = {{A trait-based test for habitat filtering: Convex hull volume}},
-volume = {87},
-year = {2006}
-}
-@article{Laughlin2012,
-abstract = {Community assembly involves two antagonistic processes that select functional traits in opposite directions. Environmental filtering tends to increase the functional similarity of species within communities leading to trait convergence, whereas competition tends to limit the functional similarity of species within communities leading to trait divergence. Here, we introduce a new hierarchical Bayesian model that incorporates intraspecific trait variation into a predictive framework to unify classic coexistence theory and evolutionary biology with recent trait-based approaches. Model predictions exhibited a significant positive correlation (r = 0.66) with observed relative abundances along a 10 °C gradient in mean annual temperature. The model predicted the correct dominant species in half of the plots, and accurately reproduced species' temperature optimums. The framework is generalizable to any ecosystem as it can accommodate any species pool, any set of functional traits and multiple environmental gradients, and it eliminates some of the criticisms associated with recent trait-based community assembly models.},
-author = {Laughlin, Daniel C. and Joshi, Chaitanya and van Bodegom, Peter M. and Bastow, Zachary A. and Ful{\'{e}}, Peter Z.},
-doi = {10.1111/j.1461-0248.2012.01852.x},
-editor = {Fukami, Tadashi},
-file = {::;::},
-isbn = {1461-0248},
-issn = {1461023X},
-journal = {Ecology Letters},
-keywords = {Assembly rules,Bark thickness,Environmental filtering,Hierarchical Bayesian model,Limiting similarity,Maximum entropy,Specific leaf area,Trait convergence,Trait divergence,Wood density},
-month = {nov},
-number = {11},
-pages = {1291--1299},
-pmid = {22906233},
-title = {{A predictive model of community assembly that incorporates intraspecific trait variation}},
-url = {http://doi.wiley.com/10.1111/j.1461-0248.2012.01852.x},
-volume = {15},
-year = {2012}
-}
-@article{Petchey2006,
-abstract = {Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Petchey, Owen L. and Gaston, Kevin J.},
-doi = {10.1111/j.1461-0248.2006.00924.x},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {1461-023X},
-issn = {1461023X},
-journal = {Ecology Letters},
-keywords = {Context dependence,Ecosystems,Functional classification,Indirect use value,Phenetics,Redundancy,Species,Species richness,Traits},
-number = {6},
-pages = {741--758},
-pmid = {16706917},
-title = {{Functional diversity: Back to basics and looking forward}},
-volume = {9},
-year = {2006}
-}
-@article{Clark2010b,
-abstract = {In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for coexistence of large numbers of competitors. Variation among individuals within populations allows species to differ in their distributions of responses to the environment, despite the fact that the populations to which they belong do not differ, on average. Results are consistent with theory predicting that coexistence depends on competition being stronger within than between species, shown here by analysis of individual-level responses to environmental fluctuation.},
-author = {Clark, James S},
-doi = {10.1126/science.1183506},
-file = {:C$\backslash$:/Users/Eric.Marcon/OneDrive/Documents/Mendeley/Clark - 2010 - in Forest Trees.pdf:pdf},
-issn = {0036-8075},
-journal = {Science},
-month = {feb},
-number = {5969},
-pages = {1129--1132},
-title = {{Individuals and the Variation Needed for High Species Diversity in Forest Trees}},
-url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1183506},
-volume = {327},
-year = {2010}
-}
-@article{Takahashi2005,
-abstract = {Leaf nitrogen content per area (N-area) is a good indicator of assimilative capacity of leaves of deciduous broad-leaved trees. This study examined the degrees of increase in Narea in response to canopy openings as leaf mass per area (LMA) and leaf nitrogen content per mass (N-mass) in saplings of eight deciduous broad-leaved tree species in Hokkaido, northern Japan. Five of the species were well-branched species with a large number of small leaves (lateral-growth type), and the other three species were less-branched species with a small number of large leaves (vertical-growth type). The degrees of increase in Narea were compared between the two crown types. In closed-canopy conditions, leaves of the vertical-growth species tended to have a lower LMA and higher N-mass than those of the lateral-growth species, which resulted in similar N-area for both. LMA increased in canopy openings in the eight species, and the degrees of increase were not largely different between the lateral- and vertical-growth species. On the contrary, N-mass was unchanged in canopy openings in the eight species. As a result, N-area of each species increased in canopy openings in proportion to the increase in LMA, and the degrees of increase in N-area were similar in the lateral- and vertical-growth species. Therefore, this study showed that the degrees of increase in N-area were not correlated with the crown architecture (i.e., the lateral- and vertical-growth types).},
-author = {Takahashi, Koichi and Seino, Tatsuyuki and Kohyama, Takashi},
-doi = {10.1007/s11284-004-0003-z},
-file = {::},
-isbn = {0912-3814},
-issn = {09123814},
-journal = {Ecological Research},
-keywords = {Canopy openings,Crown architecture,Leaf mass per area,Leaf nitrogen},
-number = {1},
-pages = {17--23},
-title = {{Plastic changes of leaf mass per area and leaf nitrogen content in response to canopy openings in saplings of eight deciduous broad-leaved tree species}},
-volume = {20},
-year = {2005}
-}
-@article{Violle2009,
-abstract = {AimsAlthough the niche concept is of prime importance in ecology, the quantification of plant species' niches remains difficult. Here we propose that plant functional traits, as determinants of species performance, may be useful tools for quantifying species niche parameters over environmental gradients. Important findingsUnder this framework, the mean trait values of a species determine its niche position along gradients, and intraspecific trait variability determines its niche breadth. This trait-based approach can provide an operational assessment of niche for a potentially large number of species, making it possible to understand and predict species niche shifts under environmental changes. We further advocate a promising method that recently appeared in the literature, which partitions trait diversity into among- and within-community components as a way to quantify the species niche in units of traits instead of environmental parameters. This approach allows the switch of the focus from ecological niches to trait niches, facilitating the examination of species coexistence along undefined environmental gradients. Altogether, the trait-based approach provides a promising toolkit for quantifying the species ecological niche and for understanding the evolution of species niche and traits.},
-author = {Violle, Cyrille and Jiang, Lin},
-doi = {10.1093/jpe/rtp007},
-file = {::},
-isbn = {1752-9921},
-issn = {17529921},
-journal = {Journal of Plant Ecology},
-keywords = {Functional diversity,Niche breadth,Niche position,Plant functional traits,Trait niche},
-month = {jun},
-number = {2},
-pages = {87--93},
-publisher = {Oxford University Press},
-title = {{Towards a trait-based quantification of species niche}},
-url = {https://academic.oup.com/jpe/article-lookup/doi/10.1093/jpe/rtp007},
-volume = {2},
-year = {2009}
-}
-@article{Long2011,
-abstract = {Specific leaf area (SLA) is a key functional trait reflecting the trade-off between resource capture and conservation, and has been identified as playing an important role in plant community assembly. Mechanistic models of community assembly state that the assemblage of species in a local community is controlled by environment filters operating on functional traits. We measured within- and among-species variation of SLA, and environmental conditions in a tropical cloud forest to explore how variation in this functional trait contributes to community assembly. SLA variation at the species level was also decomposed into alpha (within assemblage variation), and beta (across assemblage variation) values. SLA decreased with increasing solar irradiance (approximated using plant height) within the three study sites, and differed among the three sites both for within- and among-species comparisons. Mean plot SLA, accounting for both within and among species across the three sites, increased significantly in relation to air temperature but not local photosynthetic photon flux density and soil total phosphorus. Alpha SLA decreased with increasing solar irradiance within the three sites and beta SLA differed among the three sites. Our results clearly demonstrate that light and air temperature are key environmental factors involved in organizing plant species within and among communities in tropical cloud forests. The strong relationship between both intra- and interspecific variation in SLA and environmental conditions strongly confirms the role of trait variation in the assembly of plant species in tropical cloud forest communities via environment filtering related to light availability and air temperature.},
-author = {Long, Wenxing and Zang, Runguo and Schamp, Brandon S. and Ding, Yi},
-doi = {10.1007/s00442-011-2050-9},
-file = {::},
-isbn = {0029-8549},
-issn = {00298549},
-journal = {Oecologia},
-keywords = {Air temperature,Environmental filtering,Solar irradiance,Species assemblage,Trait variation},
-number = {4},
-pages = {1103--1113},
-pmid = {21695546},
-title = {{Within- and among-species variation in specific leaf area drive community assembly in a tropical cloud forest}},
-volume = {167},
-year = {2011}
-}
-@article{Lavorel2007,
-abstract = {Sandra Lavorel, Sandra D{\'{i}}az, J. Hans C. Cornelissen, Eric Garnier, Sandy P. Harrison, Sue McIntyre, Juli G. Pausas, Natalia P{\'{e}}rez-Harguindeguy, Catherine Roumet, Carlos Urcelay},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Lavorel, Sandra and D{\'{i}}az, Sandra and Cornelissen, J Hans C and Garnier, Eric and Harrison, Sandy P and Mcintyre, Sue and Pausas, Juli G and P{\'{e}}rez-Harguindeguy, Natalia and Roumet, Catherine and Urcelay, Carlos},
-doi = {10.1300/J035v16n03_03},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {9783540327295},
-issn = {8756-8225},
-journal = {Terrestrial ecosystems in a changing world},
-number = {i},
-pages = {149--160},
-pmid = {107},
-title = {{Plant functional types: are we getting any closer to the Holy Grail?}},
-url = {http://link.springer.com/chapter/10.1007/978-3-540-32730-1{\_}13},
-year = {2007}
-}
-@misc{Albert2015,
-abstract = {Intraspecific trait variability (ITV) plays a central part in various ecological pro-cesses, though using mean trait values may be sufficient in some instances. Ecol-ogists need thus to find under which circumstances. Carlucci et al. (2015, this issue) bring new evidence on the importance of ITV for community assembly across a strong gradient. Sampling design may affect ITV quantification across gradients. Over the last years, growing evidence has accumulated on the fundamental role intraspecific trait variability (ITV) plays on ecological and evolutionary processes. Moving beyond the use of mean trait values may improve our understanding of processes acting within and among com-munities (Violle et al. 2012). However, given that (1) eco-logical field work cannot be exhaustive, (2) ITV generally contributes less to trait variance than interspecific differ-ences, and (3) ITV is rarely documented in trait databases, it has become critical to identify those circumstances under which ITV should not be neglected (Albert et al. 2011). Dealing with understory sapling communities across a canopy openness gradient in Brasil, Carlucci et al. (2015) bring new evidence to this debate. We may deplore that only specific leaf area (SLA) was measured, traits being known to be unevenly variable (Albert et al. 2010; Kichenin et al. 2013). However, they nicely explore the partition of variance both irrespective of community com-position and across the gradient, compare the response of the trait mean (CWM) and variance (FD), and compare the effect of ITV within (ITV within) and among (ITV among) communities. In this study, accounting for ITV enhances both mean plant responses and niche partitioning along the gradient. While ITV contributes less to trait variance than interspecific differences, it still disproportionately counts for revealing community patterns that otherwise could be misinterpreted (Jung et al. 2010). This reinforces the view that representing less than half of trait variation is not meaningful enough to serve as the criterion for decid-ing when ignoring ITV is reasonable (Albert et al. 2011). Four of their results are of specific interest. First, Carlucci et al. (2015) found ITV among to be much more important than ITV within for the variation in FD across the gradient. In previous studies a large part of ITV occurred within communities (Albert et al. 2010; Messier et al. 2010). We may thus wonder whether this reduced},
-author = {Albert, Cecile H.},
-booktitle = {Journal of Vegetation Science},
-doi = {10.1111/jvs.12240},
-file = {::},
-isbn = {1654-1103},
-issn = {16541103},
-number = {1},
-pages = {7--8},
-title = {{Intraspecific trait variability matters}},
-volume = {26},
-year = {2015}
-}
-@article{Carmona2016,
-author = {Carmona, Carlos P. and de Bello, Francesco and Mason, Norman W.H. and Lep{\v{s}}, Jan},
-doi = {10.1016/j.tree.2016.02.003},
-file = {::},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-month = {may},
-number = {5},
-pages = {382--394},
-title = {{Traits Without Borders: Integrating Functional Diversity Across Scales}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534716000458},
-volume = {31},
-year = {2016}
-}
-@article{Cianciaruso2009,
-abstract = {Linking species and ecosystems often relies on approaches that consider how the traits exhibited by species affect ecosystem processes. One method is to estimate functional diversity (FD) based on the dispersion of species in functional trait space. Individuals within a species also differ, however, and an unresolved challenge is how to include such intraspecific variability in a measure of functional diversity. Our solution is to extend an existing measure to variation among individuals within species. Here, simulations demonstrate how the new measure behaves relative to one that does not include individual variation. Individual-level FD was less well associated with species richness than species-level FD in a single trait dimension, because species differed in their intraspecific variation. However, in multiple trait dimensions, there was a strong association between individual- and species-level FD and richness, because many traits result in a tight relationship between functional diversity and species richness. The correlation between the two FD measures weakened as the amount of intraspecific variability increased. Analyzing natural plant communities we found no relationship between species richness and functional diversity. In these analyses, we did not have to specify the source of intraspecific variation. In fact, the variation was only among individuals. The measure can, however, include differences in the amount of intraspecific variation at different sites, as we demonstrate. Including intraspecific variation should allow a more complete understanding of the processes that link individuals and ecosystems and provide better predictions about the consequences of extinctions for ecosystem processes.},
-author = {Cianciaruso, M V and Batalha, M A and Gaston, Kevin J and Petchey, Owen L},
-doi = {10.1890/07-1864.1},
-file = {::},
-isbn = {10.1890/07-1864.1},
-issn = {0012-9658},
-journal = {Ecology},
-keywords = {complementarity,functional classification,phenotypic diversity,plasticity,species richness},
-number = {1},
-pages = {81--89},
-pmid = {19294915},
-title = {{Including Intraspecific Variabiity in Functional Diversity}},
-volume = {90},
-year = {2009}
-}
-@article{Leps2011,
-abstract = {Ecological communities and their response to environmental gradients are increasingly being described by various measures of trait composition. Aggregated trait averages (i.e. averages of trait values of constituent species, weighted by species proportions) are popular indices reflecting the functional characteristics of locally dominant species. Because the variation of these indices along environmental gradients can be caused by both species turnover and intraspecific trait variability, it is necessary to disentangle the role of both components to community variability. For quantitative traits, trait averages can be calculated from ‘fixed' trait values (i.e. a single mean trait value for individual species used for all habitats where the species is found) or trait values for individual species specific to each plot, or habitat, where the species is found. Changes in fixed averages across environments reflect species turnover, while changes in specific traits reflect both species turnover and within-species variability in traits. Here we suggest a practical method (accompanied by a set of R functions) that, by combining ‘fixed' and ‘specific averages', disentangles the effect of species turnover, intraspecific trait variability, and their covariation. These effects can be further decomposed into parts ascribed to individual explanatory variables (i.e. treatments or environmental gradients considered). The method is illustrated with a case study from a factorial mowing and fertilization experiment in a meadow in South Bohemia. Results show that the variability decomposition differs markedly among traits studied (height, Specific Leaf Area, Leaf N, P, C concentrations, leaf and stem dry matter content), both according to the relative importance of species turnover and intraspecific variability, and also according to their response to experimental factors. Both the effect of intraspecific trait variability and species turnover must be taken into account when assessing the functional role of community trait structure. Neglecting intraspecific trait variability across habitats often results in underestimating the response of communities to environmental changes.},
-author = {Lep{\v{s}}, Jan and de Bello, Francesco and {\v{S}}milauer, Petr and Dole{\v{z}}al, Jiř{\'{i}}},
-doi = {10.1111/j.1600-0587.2010.06904.x},
-file = {::},
-isbn = {1600-0587},
-issn = {09067590},
-journal = {Ecography},
-number = {5},
-pages = {856--863},
-title = {{Community trait response to environment: Disentangling species turnover vs intraspecific trait variability effects}},
-volume = {34},
-year = {2011}
-}
-@article{Carmona2016a,
-author = {Carmona, Carlos P. and de Bello, Francesco and Mason, Norman W.H. and Lep{\v{s}}, Jan},
-doi = {10.1016/j.tree.2016.07.003},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-month = {sep},
-number = {9},
-pages = {667--669},
-title = {{The Density Awakens: A Reply to Blonder}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534716300969},
-volume = {31},
-year = {2016}
-}
-@article{violle_let_2007,
-abstract = {In its simplest definition, a trait is a surrogate of organismal performance, and this meaning of the term has been used by evolutionists for a long time. Over the last three decades, developments in community and ecosystem ecology have forced the concept of trait beyond these original boundaries, and trait-based approaches are now widely used in studies ranging from the level of organisms to that of ecosystems. Despite some attempts to fix the terminology, especially in plant ecology, there is currently a high degree of confusion in the use, not only of the term “trait” itself, but also in the underlying concepts it refers to. We therefore give an unambiguous definition of plant trait, with a particular emphasis on functional trait. A hierarchical perspective is proposed, extending the “performance paradigm” to plant ecology. “Functional traits” are defined as morpho-physio-phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival, the three components of individual performance. We finally present an integrative framework explaining how changes in trait values due to environmental variations are translated into organismal performance, and how these changes may influence processes at higher organizational levels. We argue that this can be achieved by developing “integration functions” which can be grouped into functional response (community level) and effect (ecosystem level) algorithms.},
-author = {Violle, Cyrille and Navas, Marie-Laure and Vile, Denis and Kazakou, Elena and Fortunel, Claire and Hummel, Ir{\`{e}}ne and Garnier, Eric},
-doi = {10.1111/j.0030-1299.2007.15559.x},
-file = {::},
-issn = {1600-0706},
-journal = {Oikos},
-number = {5},
-pages = {882--892},
-title = {{Let the concept of trait be functional!}},
-volume = {116},
-year = {2007}
-}
-@article{Ackerly2007,
-abstract = {Plant functional traits vary both along environmental gradients and among species occupying similar conditions, creating a challenge for the synthesis of functional and community ecology. We present a trait-based approach that provides an additive decomposition of species' trait values into alpha and beta components: beta values refer to a species' position along a gradient defined by community-level mean trait values; alpha values are the difference between a species' trait values and the mean of co-occurring taxa. In woody plant communities of coastal California, beta trait values for specific leaf area, leaf size, wood density and maximum height all covary strongly, reflecting species distributions across a gradient of soil moisture availability. Alpha values, on the other hand, are generally not significantly correlated, suggesting several independent axes of differentiation within communities. This trait-based framework provides a novel approach to integrate functional ecology and gradient analysis with community ecology and coexistence theory.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Ackerly, D. D. and Cornwell, W. K.},
-doi = {10.1111/j.1461-0248.2006.01006.x},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {1461-023X},
-issn = {1461023X},
-journal = {Ecology Letters},
-keywords = {Community assembly,Functional diversity,Height,Leaf size,Niche breadth,Plant strategies,Plasticity,Seed size,Specific leaf area,Wood density},
-number = {2},
-pages = {135--145},
-pmid = {17257101},
-title = {{A trait-based approach to community assembly: Partitioning of species trait values into within- and among-community components}},
-volume = {10},
-year = {2007}
-}
-@misc{Blonder2017,
-abstract = {Hutchinson's n -dimensional hypervolume concept for the interpretation of niches as geometric shapes has provided a foundation for research across different fields of ecology and evolution. There is now an expanding set of applications for hypervolume concepts, as well as a growing set of statistical methods available to operationalize this concept with data. The concept has been applied to environmental, resource, functional trait, and morphometric axes and to different scales, i.e. from individuals, species, to communities and clades. Further, these shapes have been variously interpreted as niches, ecological or evolutionary strategy spaces, or proxies for community structure. This paper highlights these applications' shared mathematical framework, surveys uses of the hypervolume concept across fields, discusses key limitations and assumptions of hypervolume concepts in general, provides a critical guide to available statistical estimation methods, and delineates the situations where hypervolume concepts can be useful.},
-author = {Blonder, Benjamin},
-booktitle = {Ecography},
-doi = {10.1111/ecog.03187},
-file = {::},
-issn = {16000587},
-title = {{Hypervolume concepts in niche- and trait-based ecology}},
-url = {http://benjaminblonder.org/papers/2017{\_}ECOG.pdf},
-year = {2017}
-}
-@article{Jung2010,
-abstract = {P{\textgreater}1. Trait-based approaches applied to community ecology have led to a considerable advance in understanding the effect of environmental filters on species assembly. Although plant traits are known to vary both between and within species, little is known about the role of intraspecific trait variability in the non-random assembly mechanisms controlling the coexistence of species, including habitat filtering and niche differentiation. 2. We investigate the role of intraspecific variability in three key functional traits - specific leaf area (SLA), leaf dry matter content (LDMC) and height - in structuring grassland communities distributed along a flooding gradient. We quantified the contribution of intraspecific variability relative to interspecific differences in the trait-gradient relationship, and we used a null model approach to detect patterns of habitat filtering and niche differentiation, with and without intraspecific variability. 3. Community mean SLA and height varied significantly along the flooding gradient and intraspecific variability accounted for 44{\%} and 32{\%}, respectively, of these trait-gradient relationships. LDMC did not vary along the gradient, with and without accounting for intraspecific variability. Our null model approach revealed significant patterns of habitat filtering and niche differentiation for SLA and height, but not for LDMC. More strikingly, considering intraspecific trait variability greatly increased the detection of habitat filtering and was necessary to detect niche differentiation processes. 4. Synthesis. Our study provides evidence for a strong role of intraspecific trait variability in community assembly. Our findings suggest that intraspecific trait variability promotes species coexistence, by enabling species to pass through both abiotic and biotic filters. We argue that community ecology would benefit from more attention to intraspecific variability.},
-author = {Jung, Vincent and Violle, Cyrille and Mondy, C{\'{e}}dric and Hoffmann, Lucien and Muller, Serge},
-doi = {10.1111/j.1365-2745.2010.01687.x},
-file = {::},
-isbn = {0022-0477},
-issn = {00220477},
-journal = {Journal of Ecology},
-keywords = {Community null model,Determinants of plant community diversity and stru,Flood meadow,Gradient analysis,Habitat filtering,Niche differentiation,Plant functional trait,Species coexistence,Trait plasticity},
-month = {jul},
-number = {5},
-pages = {1134--1140},
-pmid = {3297},
-publisher = {Blackwell Publishing Ltd},
-title = {{Intraspecific variability and trait-based community assembly}},
-url = {http://doi.wiley.com/10.1111/j.1365-2745.2010.01687.x},
-volume = {98},
-year = {2010}
-}
-@article{Cosme2017,
-abstract = {Species distributions and assemblage composition may be the result of trait selection through environmental filters. Here, we ask whether filtering of species at the local scale could be attributed to their hydraulic architectural traits, revealing the basis of hydrological micro- habitat partitioning in a Central Amazonian forest. We analyzed the hydraulic characteristics at tissue (anatomical traits, wood specific gravity (WSG)), organ (leaf area, specific leaf area (SLA), leaf area : sapwood area ratio) and whole- plant (height) levels for 28 pairs of congeneric species from 14 genera restricted to either val- leys or plateaus of a terra-firme forest in Central Amazonia. On plateaus, species had higher WSG, but lower mean vessel area, mean vessel hydraulic diameter, sapwood area and SLA than in valleys; traits commonly associated with hydraulic safety. Mean vessel hydraulic diameter and mean vessel area increased with height for both habitats, but values were higher for plateau than for valley species of the same height. Two strategies for either efficiency or safety were detected, based on vessel size or allocation to sapwood. In conclusion, contrasting hydrological conditions act as environmental filters, generating differences in species composition at the local scale. This has important implications for the prediction of species distributions under future climate change scenarios.},
-author = {Cosme, Luiza H.M. and Schietti, Juliana and Costa, Fl{\'{a}}via R.C. and Oliveira, Rafael S.},
-doi = {10.1111/nph.14508},
-file = {::},
-isbn = {1469-8137},
-issn = {14698137},
-journal = {New Phytologist},
-keywords = {environmental filters,functional trade-offs,plant traits,topographical and hydrological conditions,tropical forest,wood anatomy,wood specific gravity},
-number = {1},
-pages = {113--125},
-title = {{The importance of hydraulic architecture to the distribution patterns of trees in a central Amazonian forest}},
-volume = {215},
-year = {2017}
-}
-@article{Clark2010,
-abstract = {In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for coexistence of large numbers of competitors. Variation among individuals within populations allows species to differ in their distributions of responses to the environment, despite the fact that the populations to which they belong do not differ, on average. Results are consistent with theory predicting that coexistence depends on competition being stronger within than between species, shown here by analysis of individual-level responses to environmental fluctuation.},
-author = {Clark, James S.},
-doi = {10.1126/science.1183506},
-file = {::},
-isbn = {0036-8075},
-issn = {0036-8075},
-journal = {Science},
-number = {5969},
-pages = {1129--1132},
-pmid = {20185724},
-title = {{Individuals and the Variation Needed for High Species Diversity in Forest Trees}},
-url = {http://science.sciencemag.org/content/327/5969/1129 http://www.sciencemag.org/cgi/doi/10.1126/science.1183506},
-volume = {327},
-year = {2010}
-}
-@article{Clark2010a,
-abstract = {High biodiversity of forests is not predicted by traditional models, and evidence for trade-offs those models require is limited. High-dimensional regulation (e.g.. N factors to regulate N species) has long been recognized as a possible alternative explanation, but it has not be been seriously pursued, because only a few limiting resources are evident for trees, and analysis of multiple interactions is challenging. We develop a hierarchical model that allows us to synthesize data from long-term, experimental; data sets with processes that control growth, maturation, fecundity, and survival. We allow for uncertainty at all stages and variation among 26 000 individuals and over time, including 268 000 tree years, for dozens of tree species. We estimate population-level parameters that apply at the species level and the interactions among latent states, i.e., the demographic rates for each individual, every year. The former show that the traditional trade-offs used to explain diversity are not present. Demographic rates overlap among species, and they do not show trends consistent with maintenance of diversity by simple mechanisms (negative correlations and limiting similarity). However, estimates of latent states at the level of individuals and years demonstrate that species partition environmental variation. Correlations between responses to variation in time are high for individuals of the same species, but not for individuals of different species. We demonstrate that these relationships are pervasive, providing strong evidence that high-dimensional regulation is critical for biodiversity regulation.},
-author = {Clark, James S. and Bell, David and Chu, Chengjin and Courbaud, Benoit and Dietze, Michael and Hersh, Michelle and Hillerislambers, Janneke and Ib{\'{a}}{\~{n}}ez, In{\'{e}}s and Ladeau, Shannon and McMahon, Sean and Metcalf, Jessica and Mohan, Jacqueline and Moran, Emily and Pangle, Luke and Pearson, Scott and Salk, Carl and Shen, Zehao and Valle, Denis and Wyckoff, Peter},
-doi = {10.1890/09-1541.1},
-file = {::},
-isbn = {0012-9615},
-issn = {00129615},
-journal = {Ecological Monographs},
-keywords = {Bayesian analysis,Biodiversity,Coexistence,Competition,Forest dynamics,Hierarchical models},
-month = {nov},
-number = {4},
-pages = {569--608},
-publisher = {Ecological Society of America},
-title = {{High-dimensional coexistence based on individual variation: A synthesis of evidence}},
-url = {http://doi.wiley.com/10.1890/09-1541.1},
-volume = {80},
-year = {2010}
-}
-@article{Geber2003b,
-abstract = {We surveyed the literature published since 1985 for evidence of natural selection and heritability in vegetative functional traits and performance. Our goals were to (1) review patterns of selection on specific functional traits and (2) assess general evolutionary questions about selection and heritability for broad classes of traits. While generalizations about the functional significance of specific traits are premature, several functional hypotheses are supported. For example, herbivores can exert strong selection on secondary chemistry and mechanical defenses, but costs of resistance and negative correlations between defense traits may constrain their evolution. Competitive interactions select for early germination and favor stem elongation and shifts in flowering time where such responses actually minimize competitive effects. In the very few studies of physiology, selection on gas exchange and leaf size is clearly environment dependent. More generally, in reciprocal transplant experiments, populations often are locally adapted, and selection favors the native phenotype. These results suggest that selection is important in functional trait evolution and population differentiation. At the same time, selection often varies in space and time and across life-history episodes. This variation could slow the rate of evolutionary change, maintain genetic variation within populations, and select for plasticity. Analyses of general questions revealed that indirect selection through correlated characters accounts for a substantial portion of total selection on traits and often appears to reinforce the pattern of direct selection. This could be due to environmental effects on multiple phenotypic traits and fitness. Alternatively, indirect selection could contribute to the rapid evolution of suites of traits. We found only weak evidence that traits under strong selection have low heritability, a pattern that has been reported for animals and predicted by some theory. Thus, the rate of evolutionary change may well differ among traits. The strength of selection also depended on the fitness measure, being stronger selection through cumulative fitness than fertility or vegetative performance. Attributes of species' biology and experimental design affected selection and heritability estimates. Heritability was lower in inbreeding species relative to outbreeders, as expected. Heritabilities in controlled environments substantially overestimate estimates from the wild and should not be used as reliable predictors of the rate of adaptive evolutionary change in natural populations. Likewise, broad-sense heritability overestimates narrow-sense heritability and is thus unreliable for predicting evolutionary change in outbreeding species. Future studies of functional trait evolution should focus on physiology and a broader array of phenological and developmental traits. Long-lived species are severely underrepresented in microevolutionary studies, no doubt for practical reasons. Finally, an emphasis should be placed on exploring the nature and effect of trait interactions on fitness, since these are likely to be very important in shaping the course of evolution.},
-author = {Geber, Monica A. and Griffen, Lauren R.},
-doi = {10.1086/368233},
-file = {::},
-isbn = {1058-5893},
-issn = {1058-5893},
-journal = {International Journal of Plant Sciences},
-keywords = {adaptation,direct selection,evolution,fitness,genetic variation,heritability,indirect selection,performance,selection coefficients},
-number = {S3},
-pages = {S21--S42},
-pmid = {184018500003},
-title = {{Inheritance and Natural Selection on Functional Traits}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/368233},
-volume = {164},
-year = {2003}
-}
-@article{Aarssen1983,
-abstract = {The common assumption that species coexistence in nature can be generally explained by processes of natural selection for niche differentiation does not have strong empirical support for plants. The meaning of competitive ability has traditionally been embedded within an Eltonian view of the niche. In particular reference to plants, however, a true distinction between the meanings of niche and competitive ability is established based on the premise that for one species to competitively exclude another, two distinct conditions must be satisfied: (1) There must be a sufficient degree of overlap in the niche requirements of the two species; and (2) one species must be sufficiently superior at reducing the availability of resources to the other. Following these considerations an evolutionary theory of coexistence is proposed involving two alternative mechanisms based on a broader interpretation of the operation of natural selection in systems of competition than previously recognized. Competitive exclusion may be avoided either if natural selection results in niche differentiation (selection for ecological combining ability), or if reciprocal selection maintains a balance of competitive abilities (selection for competitive combining ability). Competitive combining ability, although previously overlooked, has wide applicability to plants for which coexistence frequently is explained incompletely by ecological combining ability. The main argument is as follows: All biological attributes of a species will play a part in determining its niche requirements on the one hand, and its relative competitive ability for those requirements on the other. Given the assumption that niche requirements generally overlap broadly in plants, I propose that coexistence is permitted because there are numerous possible permutations and combinations of biological attributes in plants which are roughly equivalent in the overall competitive power which they confer. In selection for competitive combining ability, these attribute complexes are continually adjusted in an ongoing process of coevolution in which local neighborhoods are constantly engaged in a fine-tuning process that alters the way members respond to one another. Consequently, natural selection ultimately maintains a balance of overall relative competitive abilities between two species for essentially the same contested resources. I discuss the relevance of this mechanism and its relationship to other theories and concepts associated with coexistence in contexts of competition. It is proposed that, in nature, selection for ecological combining ability and selection for competitive combining ability operate in concert, and this provides reconciliation of the contradiction in theory between convergent adaptation to a common habitat and divergent adaptation to other members of the community.},
-author = {Aarssen, Lonnie W.},
-doi = {10.1086/284167},
-isbn = {0003-0147},
-issn = {0003-0147},
-journal = {The American Naturalist},
-month = {dec},
-number = {6},
-pages = {707--731},
-pmid = {8},
-publisher = {University of Chicago Press},
-title = {{Ecological Combining Ability and Competitive Combining Ability in Plants: Toward a General Evolutionary Theory of Coexistence in Systems of Competition}},
-url = {http://www.journals.uchicago.edu/doi/10.1086/284167},
-volume = {122},
-year = {1983}
-}
-@article{Des2015,
-author = {Des, Etat and Unis, Etats and Washington, St N W},
-file = {::},
-number = {November},
-pages = {812--814},
-title = {{From Plant Traits to Plant Communities :}},
-year = {2015}
-}
-@article{Blonder2016,
-author = {Blonder, Benjamin},
-doi = {10.1016/j.tree.2016.07.001},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-month = {sep},
-number = {9},
-pages = {665--667},
-title = {{Pushing Past Boundaries for Trait Hypervolumes: A Response to Carmona et al.}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534716300945},
-volume = {31},
-year = {2016}
-}
-@article{Blonder2014,
-abstract = {Aim The Hutchinsonian hypervolume is the conceptual foundation for many lines of ecological and evolutionary inquiry, including functional morphology, comparative biology, community ecology and niche theory. However, extant methods to sample from hypervolumes or measure their geometry perform poorly on high-dimensional or holey datasets. Innovation We first highlight the conceptual and computational issues that have prevented a more direct approach to measuring hypervolumes. Next, we present a new multivariate kernel density estimation method that resolves many of these problems in an arbitrary number of dimensions. Main conclusions We show that our method (implemented as the ‘hypervolume' R package) can match several extant methods for hypervolume geometry and species distribution modelling. Tools to quantify high-dimensional ecological hypervolumes will enable a wide range of fundamental descriptive, inferential and comparative questions to be addressed.},
-author = {Blonder, Benjamin and Lamanna, Christine and Violle, Cyrille and Enquist, Brian J.},
-doi = {10.1111/geb.12146},
-file = {::},
-isbn = {1466822X},
-issn = {14668238},
-journal = {Global Ecology and Biogeography},
-keywords = {Environmental niche modelling,Hole,Hutchinson,Hypervolume,Kernel density estimation,Morphospace,Niche,Niche overlap,Species distribution modelling},
-number = {5},
-pages = {595--609},
-title = {{The n-dimensional hypervolume}},
-volume = {23},
-year = {2014}
-}
-@article{Messier2017a,
-abstract = {1.Plant phenotypic diversity is shaped by the interplay of trade-offs and constraints in evolution. Closely integrated groups of traits (i.e. trait dimensions) are used to classify plant phenotypic diversity into plant strategies, but we do not know the degree of interdependence among trait dimensions. To assess how selection has shaped the phenotypic space, we examine whether trait dimensions are independent.2.We gathered data on saplings of 24 locally coexisting tree species in a temperate forest, and examined the correlation structure of 20 leaf, branch, stem and root traits. These traits fall into three well-established trait dimensions (the leaf economic spectrum, the wood spectrum, and Corner's Rules) that characterize vital plant functions: resource acquisition, sap transport, mechanical support and canopy architecture. Using ordinations, network analyses and Mantel tests, we tested whether the sapling phenotype of these tree species is organized along independent trait dimensions.3.Across species, the sapling phenotype is not structured into clear trait dimensions. The trait relationships defining the trait dimensions are weak and do not dominate the correlation structure of the sapling phenotype as a whole. Instead traits from the three commonly recognized trait dimensions are organized into an integrated trait network. The effect of phylogeny on trait correlations is minimal.4.Our results indicate that trait dimensions apparent in broad-based interspecific surveys do not hold up among locally coexisting species. Furthermore, architectural traits appear central to the phenotypic network, suggesting a pivotal role for branching architecture in linking resource acquisition, mechanical support and hydraulic functions.5.Synthesis. Our study indicates that local and global patterns of phenotypic integration differ and calls into question the use of trait dimensions at local scales. We propose that a network approach to assessing plant function more effectively reflects the multiple trade-offs and constraints shaping the phenotype in locally co-occurring species.This article is protected by copyright. All rights reserved.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:physics/0608246v3},
-author = {Messier, Julie and Lechowicz, Martin J. and McGill, Brian J. and Violle, Cyrille and Enquist, Brian J.},
-doi = {10.1111/1365-2745.12755},
-editor = {Cornelissen, Hans},
-eprint = {0608246v3},
-file = {::},
-isbn = {4955139574},
-issn = {13652745},
-journal = {Journal of Ecology},
-keywords = {Corner's Rules,architecture,ecophysiology,functional ecology,leaf economic spectrum,local scale,phenotypic integration,trait dimensions,trees,wood spectrum},
-month = {nov},
-number = {6},
-pages = {1775--1790},
-pmid = {28199780},
-primaryClass = {arXiv:physics},
-title = {{Interspecific integration of trait dimensions at local scales: the plant phenotype as an integrated network}},
-url = {http://doi.wiley.com/10.1111/1365-2745.12755},
-volume = {105},
-year = {2017}
-}
-@article{chave_towards_2009,
-author = {Chave, Jerome and Coomes, David and Jansen, Steven and Lewis, Simon L and Swenson, Nathan G and Zanne, Amy E},
-doi = {10.1111/j.1461-0248.2009.01285.x},
-file = {::},
-issn = {1461023X, 14610248},
-journal = {Ecology Letters},
-number = {4},
-pages = {351--366},
-title = {{Towards a worldwide wood economics spectrum}},
-url = {http://doi.wiley.com/10.1111/j.1461-0248.2009.01285.x},
-volume = {12},
-year = {2009}
-}
-@article{Lortie2004a,
-abstract = {Plant communities have traditionally been viewed as either a random collection of individuals or as organismal entities. For most ecologists however, neither perspective provides a modern comprehensive view of plant communities, but we have yet to formalize the view that we currently hold. Here, we assert that an explicit re-consideration of formal community theory must incorporate interactions that have recently been prominent in plant ecology, namely facilitation and indirect effects among competitors. These interactions do not suppport the traditional individualistic perspective. We believe that rejecting strict individualistic theory will allow ecologists to better explain variation occurring at different spatial scales, synthesize more general predictive theories of community dynamics, and develop models for community-level responses to global change. Here, we introduce the concept of the integrated community (IC) which proposes that natural plant communities range from highly individualistic to highly interdependent depending on synergism among: (i) stochastic processes, (ii) the abiotic tolerances of species, (iii) positive and negative interactions among plants, and (iv) indirect interactions within and between trophic levels. All of these processes are well accepted by plant ecologists, but no single theory has sought to integrate these different processes into our concept of communities},
-author = {Lortie, Christopher J. and Brooker, Rob W. and Choler, Philippe and Kikvidze, Zaal and Michalet, Richard and Pugnaire, Francisco I. and Callaway, Ragan M.},
-doi = {10.1111/j.0030-1299.2004.13250.x},
-file = {::},
-isbn = {0030-1299},
-issn = {00301299},
-journal = {Oikos},
-number = {2},
-pages = {433--438},
-pmid = {2950},
-title = {{Rethinking plant community theory}},
-volume = {107},
-year = {2004}
-}
-@article{Albert2010b,
-abstract = {P{\textgreater}1. Functional traits have been extensively used to describe, group and$\backslash$nrank species according to their functions. There is now growing evidence$\backslash$nthat intraspecific functional variability, as well as interspecific$\backslash$nvariability, can have significant effects on community dynamics and$\backslash$necosystem functioning. A core hypothesis for the use of functional$\backslash$ntraits expressed as species means, that their intraspecific variability$\backslash$nis negligible compared with their interspecific variability, has however$\backslash$nbeen too rarely tested empirically. We then addressed four questions: Is$\backslash$nintraspecific functional variability across species ranges negligible$\backslash$ncompared with interspecific variability? Are the major resource$\backslash$neconomics trade-off and functional strategies robust to individual trait$\backslash$nvariability? Are species rankings or ordination robust across species$\backslash$nranges once considering intraspecific variability? Can species be$\backslash$ndiscriminated by their leaf traits?$\backslash$n2. Using an environmentally stratified sampling design within an alpine$\backslash$ncatchment, we collected five functional traits for 13 common plant$\backslash$nspecies with contrasting life histories and traits. Several populations$\backslash$nfrom a range of environmental conditions were then sampled for each$\backslash$nspecies across their ranges.$\backslash$n3. With an original combination of single-trait and multi-trait$\backslash$nanalyses, we highlighted a non-negligible contribution of intraspecific$\backslash$nvariability to overall functional trait variability (similar to 30{\%}).$\backslash$nAlthough not affecting general and well-known functional trade-offs and$\backslash$nstrategies, intraspecific functional variability had the potential to$\backslash$nalter species ordination and produced a functional continuum rather than$\backslash$na clear-cut species classification.$\backslash$n4. Deciding whether intraspecific functional variability can be$\backslash$nconsidered as negligible - species being represented by mean trait$\backslash$nvalues -, or not - species being represented by multivariate trait$\backslash$ndistributions -, is an essential question for multiple ecological$\backslash$nissues. However, this decision cannot be generic, but will depend on the$\backslash$nstudied system and selected traits and species, as well as on study$\backslash$nobjectives.},
-author = {Albert, C{\'{e}}cile H{\'{e}}l{\`{e}}ne and Thuiller, Wilfried and Yoccoz, Nigel Gilles and Douzet, Rolland and Aubert, Serge and Lavorel, Sandra},
-doi = {10.1111/j.1365-2435.2010.01727.x},
-file = {::},
-isbn = {1365-2435},
-issn = {02698463},
-journal = {Functional Ecology},
-keywords = {Alpine ecosystems,Environmental gradients,Functional strategies,Interspecific and intraspecific variability,Leaf economics spectrum,Linear mixed models,Plant functional traits,Species ranking},
-number = {6},
-pages = {1192--1201},
-pmid = {21808771},
-title = {{A multi-trait approach reveals the structure and the relative importance of intra- vs. interspecific variability in plant traits}},
-volume = {24},
-year = {2010}
-}
-@article{Messier2017,
-abstract = {Trait-based approaches have an increasingly dominant role in community ecology. Although trait-based strategy dimensions such as the leaf economic spectrum (LES) have been identified primarily at global-scales, trait variation at the community scale is often interpreted in this context. Here we argue from several lines of evidence that a research priority should be to determine whether global- scale trait relationships hold at more local scales. We review recent literature assessing trait variation at smaller scales, and then present a case study exploring the relationship between the correlation strength of leaf traits and their similarity in variation structure across ecological scales. We find that the correlation strength between pairs of leaf traits does not predict whether the traits respond similarly to different drivers of variation. Instead, correlation strength only sets an upper bound to the dissimilarity in trait variation structure. With moderate correlation strengths, LES traits largely retain the ability to respond independently to different drivers of phenotypic variation at different scales. Recent literature and our results suggest that LES relationships may not hold at local scales. Clarifying under what conditions and at which scales the LES is consistently expressed is necessary for us to make the most of the emerging trait toolbox.},
-archivePrefix = {arXiv},
-arxivId = {10.1111/ecog.02097},
-author = {Messier, Julie and McGill, Brian J. and Enquist, Brian J. and Lechowicz, Martin J.},
-doi = {10.1111/ecog.02006},
-eprint = {ecog.02097},
-file = {::},
-isbn = {6503251521},
-issn = {16000587},
-journal = {Ecography},
-number = {6},
-pages = {685--697},
-pmid = {26044706},
-primaryClass = {10.1111},
-title = {{Trait variation and integration across scales: is the leaf economic spectrum present at local scales?}},
-volume = {40},
-year = {2017}
-}
-@book{Garnier2012,
-abstract = {Comparative functional ecology seeks to understand why and how ecological systems and their components operate differently across environments. Although traditionally used in (semi)-natural situations, its concepts and methods could certainly apply to address key issues in the large variety of agricultural systems encountered across the world. In this review, we present major advances in comparative plant functional ecology that were made possible over the last two decades by the rapid development of a trait-based approach to plant functioning and prospects to apply it in agricultural situations. The strength of this approach is that it enables us to assess the interactions between organisms and their environment simultaneously on a large number of species, a prerequisite to address questions relative to species distribution, community assembly and ecosystem functioning. The trait concept will be first defined, before presenting a conceptual framework to understand the effects of environmental factors on plant community structure and ecosystem properties via plant traits. We will then argue that leading dimensions of variation among species can be captured by some selected traits and show that a combination of three easily measured traits—specific leaf area (the ratio of leaf area to leaf dry mass), plant height and seed mass—enables us to assess how different species use their resources, interact with neighbours and disperse in time and space. The use of traits to address central questions in community ecology will be reviewed next. It will be shown that traits allow us to (1) understand how plant species are sorted according to the nature of environmental gradients, (2) evaluate the relative importance of habitat filtering and limiting similarity in the process of community assembly and (3) quantify two main components of community functional structure, namely, community-weighted means of traits and community functional divergence. The relative impacts of these two components on ecosystem properties will then be discussed in the case of several components of primary productivity, litter decomposition, soil water content and carbon sequestration. There is strong support for the biomass ratio hypothesis, which states that the extent to which the traits of a species affect those ecosystem properties depends on the abundance of this species in the community. Assessing the role of functional divergence among species on ecosystem properties will require major methodological breakthroughs, both in terms of metrics and statistical procedures to be used. In agricultural situations, we show that trait-based approaches have been successfully developed to assess the impacts of management practices on (1) the agronomic value of grasslands and (2) the functional composition and structure of crop weed communities and how these could affect the functioning of the crop. Applications in forestry are still poorly developed, especially in temperate regions where the number of species in managed forest remains relatively low. The last decades of research have led to the constitution of large data sets of plant traits, which remain poorly compatible and accessible. Recent advances in the field of ecoinformatics suggest that major progress could be achieved in this area by using improved metadata standards and advancing trait domain ontologies. Finally, concluding remarks, unanswered questions and directions for research using the functional approach to biodiversity made possible by the use of traits will be discussed in the contexts of ecological and agronomical systems. The latter indeed cover a wide range of environmental conditions and biological diversity, and the prospect for reducing environmental impacts in highly productive, low- diversity systems will certainly imply improving our skills for the management of more diverse systems prone to a trait-based approach as reviewed here.},
-author = {Garnier, Eric and Navas, Marie Laure},
-booktitle = {Agronomy for Sustainable Development},
-doi = {10.1007/s13593-011-0036-y},
-file = {::},
-isbn = {1359301100},
-issn = {17740746},
-keywords = {Agroecology,Biodiversity,Community structure,Comparative ecology. Ecoinformatics,Ecological strategy,Ecosystem properties,Environmental conditions,Functional diversity. Plant functional trait},
-number = {2},
-pages = {365--399},
-title = {{A trait-based approach to comparative functional plant ecology: Concepts, methods and applications for agroecology. A review}},
-volume = {32},
-year = {2012}
-}
-@article{Laughlin2015b,
-abstract = {Every species on Earth fills a unique environmental niche that is driven, in part, by the process of environmental filtering, where the adaptive value of the functional traits of individuals determine their fitness within the given environmental conditions. Despite its long-standing importance in ecology, theoretical investigations of environmental filtering have lagged behind studies of species interactions and neutral dynamics. A new statistical model of trait-based environmental filtering can be a useful tool for exploring the logical consequences of this process while holding all other processes constant. The model uses the logic of objective Bayesian inference to compute the probabilities of species within different environments using two sources of information: the location and dispersion of species within functional trait space, and the statistical relationship between traits and environmental gradients. By varying key parameters in the model, we highlight several testable hypotheses for trait-based ecology. First, niche breadth decreases as intraspecific trait variation decreases, as the strength of the environmental filter increases, and if the trait values do not enhance fitness in any environmental condition in the landscape. Second, niche shape is determined by the form of the trait-environment relationships, where species with extreme trait values are predicted to dominate at the environmental extremes when traits are linearly related to the environment, species with intermediate trait values generally have a selective advantage across a broader environmental range, and bimodal species response curves can occur independently from negative species interactions. The generality of these modelling results can be tested using empirical data from any ecosystem.},
-author = {Laughlin, Daniel C. and Joshi, Chaitanya},
-doi = {10.1016/j.ecolmodel.2015.03.013},
-file = {::},
-isbn = {0304-3800},
-issn = {03043800},
-journal = {Ecological Modelling},
-keywords = {Community assembly,Functional traits,Habitat filtering,Predictive model,Species distribution modelling,Trait convergence},
-month = {jul},
-pages = {10--21},
-publisher = {Elsevier},
-title = {{Theoretical consequences of trait-based environmental filtering for the breadth and shape of the niche: New testable hypotheses generated by the Traitspace model}},
-url = {https://www.sciencedirect.com/science/article/pii/S0304380015001246},
-volume = {307},
-year = {2015}
-}
-@article{Callaway2003,
-author = {Callaway, Ragan M. and Pennings, Steven C. and Richards, Christina L. and Ecology, Source and May, No},
-doi = {10.1890/0012-9658(2003)084[1115:PPAIAP]2.0.CO;2},
-file = {::},
-issn = {1939-9170},
-journal = {America},
-keywords = {allelopathy,chemical defense,clonal morphology,competition,facilitation,ge-,herbiv-,induced resistance,notype to produce different,ory,phenotypic plasticity,phenotypic plasticity is the,physiological or morpho-,plant interactions,property of a given,roots},
-month = {may},
-number = {5},
-pages = {1115--1128},
-publisher = {Ecological Society of America},
-title = {{Phenotypic Plasticity and Interactions among Plants}},
-url = {http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2003)084[1115:PPAIAP]2.0.CO;2/full},
-volume = {84},
-year = {2012}
-}
-@article{Lajoie2015,
-abstract = {Intraspecific trait variation (ITV) plays a potentially important role in determining functional community composition across environmental gradients. However, the importance of ITV varies greatly among studies, and we lack a coherent understanding of the contexts under which to expect a high versus low contribution of ITV to trait-environment matching among communities. Here we first elaborate a novel conceptual framework posing specific hypotheses and predictions about the environmental and ecological contexts underlying the contribution of ITV to community trait turnover. We then empirically test these predictions in understory herbaceous plant communities in a montane environment, for 3 functional traits (flowering phenology, specific leaf area and height). We found that different components of trait variation mapped onto different environmental axes, specifically reporting a greater contribution of ITV along non-climatic axes (e.g., soil properties, light) than along the main climatic axis (i.e., ele...},
-author = {Lajoie, Genevi{\`{e}}ve and Vellend, Mark},
-doi = {10.1890/15-0156.1.sm},
-file = {::},
-isbn = {1939-9170},
-issn = {00129658},
-journal = {Ecology},
-keywords = {Community ecology,Elevation,Environmental gradients,Intraspecific variation,Plant functional traits,Species turnover,Trait-abundance-environment relationship},
-number = {11},
-pages = {2912--2922},
-title = {{Understanding context dependence in the contribution of intraspecific variation to community trait-environment matching}},
-url = {http://mvellend.recherche.usherbrooke.ca/Lajoie{\&}Vellend{\_}Ecology2015.pdf},
-volume = {96},
-year = {2015}
-}
-@article{Wright2005a,
-abstract = {Aim Our aim was to quantify climatic influences on key leaf traits and relationships at the global scale. This knowledge provides insight into how plants have adapted to different environmental pressures, and will lead to better calibration of future vegetation-climate models. Location The data set represents vegetation from 175 sites around the world. Methods For more than 2500 vascular plant species, we compiled data on leaf mass per area (LMA), leaf life span (LL), nitrogen concentration (N(mass)) and photosynthetic capacity (A(mass)). Site climate was described with several standard indices. Correlation and regression analyses were used for quantifying relationships between single leaf traits and climate. Standardized major axis (SMA) analyses were used for assessing the effect of climate on bivariate relationships between leaf traits. Principal components analysis (PCA) was used to summarize multidimensional trait variation. Results At hotter, drier and higher irradiance sites, (1) mean LMA and leaf N per area were higher; (2) average LL was shorter at a given LMA, or the increase in LL was less for a given increase in LMA (LL-LMA relationships became less positive); and (3) A(mass) was lower at a given N(mass), or the increase in A(mass) was less for a given increase in N(mass). Considering all traits simultaneously, 18{\%} of variation along the principal multivariate trait axis was explained by climate. Main conclusions Trait-shifts with climate were of sufficient magnitude to have major implications for plant dry mass and nutrient economics, and represent substantial selective pressures associated with adaptation to different climatic regimes.},
-author = {Wright, Ian J. and Reich, Peter B. and Cornelissen, Johannes H C and Falster, Daniel S. and Groom, Philip K. and Hikosaka, Kouki and Lee, William and Lusk, Christopher H. and Niinemets, {\"{U}}lo and Oleksyn, Jacek and Osada, Noriyuki and Poorter, Hendrik and Warton, David I. and Westoby, Mark},
-doi = {10.1111/j.1466-822x.2005.00172.x},
-file = {::},
-isbn = {1466-822X(print); 1466-8328(electronic)},
-issn = {1466822X},
-journal = {Global Ecology and Biogeography},
-keywords = {Irradiance,Leaf life span,Leaf mass per area,Nitrogen,Photosynthesis,Plant strategies,Rainfall,Temperature},
-number = {5},
-pages = {411--421},
-title = {{Modulation of leaf economic traits and trait relationships by climate}},
-volume = {14},
-year = {2005}
-}
-@article{westoby_leaf-height-seed_1998,
-author = {Westoby, Mark},
-file = {::},
-journal = {Plant and soil},
-number = {2},
-pages = {213--227},
-title = {{A leaf-height-seed ({\{}LHS{\}}) plant ecology strategy scheme}},
-volume = {199},
-year = {1998}
-}
-@article{Bolnick2011,
-abstract = {Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution. {\textcopyright} 2011 Elsevier Ltd.},
-author = {Bolnick, Daniel I. and Amarasekare, Priyanga and Ara{\'{u}}jo, M{\'{a}}rcio S. and B{\"{u}}rger, Reinhard and Levine, Jonathan M. and Novak, Mark and Rudolf, Volker H.W. and Schreiber, Sebastian J. and Urban, Mark C. and Vasseur, David A.},
-doi = {10.1016/j.tree.2011.01.009},
-file = {::},
-isbn = {0169-5347},
-issn = {01695347},
-journal = {Trends in Ecology and Evolution},
-number = {4},
-pages = {183--192},
-pmid = {21367482},
-title = {{Why intraspecific trait variation matters in community ecology}},
-volume = {26},
-year = {2011}
-}
-@article{Paine2010,
-abstract = {1. The complex structure of tree bark reflects its many functions, which include structural support as well as defence against fire, pests and pathogens. Thick bark, however, might limit respiration by the living tissues of the trunk. Nevertheless, little research has addressed commu- nity-level variation in bark thickness, and to the best of our knowledge, no one has tested multi- ple hypotheses to explain variation in bark thickness. 2. We conducted an extensive survey of bark thickness within and among species of trees in the tropical rain forests of French Guiana. Trunk bark thickness increased by 1{\AE}2 mm per 10 cm increase in stem diameter, and varied widely at all taxonomic levels. Mean trunk bark thickness was 4{\AE}5 mm(range: 0{\AE}5–29 mm), which was less that found in two Amazonian rain forests in pre- vious studies. This survey of bark thickness should be of use for forest management since tree survival through fire is strongly predicted by bark thickness. 3. We combined the survey data with multiple datasets to test several functional hypotheses pro- posed to explain variation in bark thickness. We found bark to provide an average of 10{\%} of the flexural rigidity of tree stems, which was substantially less than that found in the only other study of bark stiffness. Bark thickness was uncorrelated with species' association with fire-prone habi- tats, suggesting that the influence of fire on bark thickness does not extend into moist Forests. There was also little evidence that bark thickness is affected by its function as a defence against herbivory. Nor was there evidence that thick bark limits trunk respiration. 4. A re-analysis of previously collected anatomical data indicated that variation in rhytidome (non-conducting outer bark) thickness explains much of the variation in overall bark thickness. As rhytidome is primarily involved in protecting the living tissues of the trunk, we suggest that bark thickness is driven mostly by its defensive function. 5. Functional explanations for the variation in bark thickness were not clear-cut. Nevertheless, this study provides a foundation for further investigation of the functional bases of bark in tropi- cal trees.},
-author = {Paine, Charles Eliot Timothy and Stahl, Cl{\'{e}}ment and Courtois, Elodie A. and Pati{\~{n}}o, Sandra and Sarmiento, Carolina and Baraloto, Christopher},
-doi = {10.1111/j.1365-2435.2010.01736.x},
-file = {::},
-isbn = {1365-2435},
-issn = {02698463},
-journal = {Functional Ecology},
-keywords = {Bark thickness,Fire ecology,Flexural rigidity,Herbivore defence,Periderm,Rhytidome,Trunk respiration},
-number = {6},
-pages = {1202--1210},
-title = {{Functional explanations for variation in bark thickness in tropical rain forest trees}},
-volume = {24},
-year = {2010}
-}
-@article{Albert2010a,
-abstract = {P{\textgreater}1. Functional traits are increasingly used to investigate community$\backslash$nstructure, ecosystem functioning or to classify species into functional$\backslash$ngroups. These functional traits are expected to be variable between and$\backslash$nwithin species. Intraspecific functional variability is supposed to$\backslash$ninfluence and modulate species responses to environmental changes and$\backslash$ntheir effects on their environment. However, this hypothesis remains$\backslash$npoorly tested and species are mostly described by mean trait values$\backslash$nwithout any consideration of variability in individual trait values.$\backslash$n2. In this study, we quantify the extent of intraspecific plant$\backslash$nfunctional trait variability, its spatial structure and its response to$\backslash$nenvironmental factors. Using a sampling design structured along two$\backslash$ndirect and orthogonal climatic gradients in an alpine valley, we$\backslash$nquantified and analysed the intraspecific variability for three$\backslash$nfunctional traits (height, leaf dry matter content and leaf nitrogen$\backslash$ncontent) measured on sixteen plant species with contrasting life$\backslash$nhistories.$\backslash$n3. Results showed a large variability of traits within species with$\backslash$nlarge discrepancies between functional traits and species. This$\backslash$nvariability did not appear to be structured within populations. Between$\backslash$npopulations, the overall variability was partly explained by the$\backslash$nselected gradients. Despite the strong effects of temperature and$\backslash$nradiation on trait intraspecific variability, the response curves of$\backslash$ntraits along gradients were partly idiosyncratic.$\backslash$n4.Synthesis. Giving a comprehensive quantification of intraspecific$\backslash$nfunctional variability through the analysis of an original data set, we$\backslash$nreport new evidence that using a single trait value to describe a given$\backslash$nspecies can hide large functional variation for this species along$\backslash$nenvironmental gradients. These findings suggest that intraspecific$\backslash$nfunctional variability should be a concern for ecologists and its$\backslash$nrecognition opens new opportunities to better understand and predict$\backslash$necological patterns in a changing environment. Further analyses are,$\backslash$nhowever, required to compare inter- and intraspecific variability.},
-archivePrefix = {arXiv},
-arxivId = {arXiv:1011.1669v3},
-author = {Albert, C{\'{e}}cile H{\'{e}}l{\`{e}}ne and Thuiller, Wilfried and Yoccoz, Nigel Gilles and Soudant, Alex and Boucher, Florian and Saccone, Patrick and Lavorel, Sandra},
-doi = {10.1111/j.1365-2745.2010.01651.x},
-eprint = {arXiv:1011.1669v3},
-file = {::},
-isbn = {0022-0477},
-issn = {00220477},
-journal = {Journal of Ecology},
-keywords = {Alpine ecosystems,Environmental gradients,Intraspecific variability,Leaf traits,Life forms,Linear mixed models,Plant functional traits,Radiation,Response surface methodology,Temperature},
-number = {3},
-pages = {604--613},
-pmid = {21861511},
-title = {{Intraspecific functional variability: Extent, structure and sources of variation}},
-volume = {98},
-year = {2010}
-}
-@article{mcgill_rebuilding_2006,
-author = {Mcgill, B and Enquist, B and Weiher, E and Westoby, M},
-doi = {10.1016/j.tree.2006.02.002},
-file = {::},
-issn = {01695347},
-journal = {Trends in Ecology {\&} Evolution},
-number = {4},
-pages = {178--185},
-title = {{Rebuilding community ecology from functional traits}},
-url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534706000334},
-volume = {21},
-year = {2006}
-}
-@article{Ackerly2000,
-author = {Ackerly, David D and Dudley, Susan A and Sultan, Sonia E and Schmitt, Johanna and Coleman, James S and Linder, C Randall and Sandquist, Darren R and Geber, Monica A and Evans, S and Dawson, Todd E and Lechowicz, Martin J},
-file = {::},
-number = {11},
-pages = {979--995},
-title = {{The Evolution of Plant Ecophysiological Traits : Recent Advances and Future Directions}},
-volume = {50},
-year = {2000}
-}